Variant report

Variant	rs4653946
Chromosome Location	chr1:228546242-228546243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228539851..228543627-chr1:228544057..228547881,6	MCF-7	breast:
2	chr1:228522476..228525116-chr1:228543673..228546282,2	MCF-7	breast:
3	chr1:228542695..228550800-chr1:228643549..228647341,10	K562	blood:
4	chr1:228545751..228548390-chr1:228548466..228551697,6	MCF-7	breast:
5	chr1:228545933..228548226-chr1:228643817..228645721,3	K562	blood:
6	chr1:228539981..228541559-chr1:228545255..228546847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10799474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150907	0.89[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs1150910	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs1150913	0.81[EUR][1000 genomes]
rs1150914	0.89[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11581897	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810627	0.80[EUR][1000 genomes]
rs1188709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188717	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188731	0.81[EUR][1000 genomes]
rs1612473	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16848509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684868	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1757160	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872740	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287609	0.81[EUR][1000 genomes]
rs287610	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs287611	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs287612	0.81[EUR][1000 genomes]
rs287614	0.89[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs287616	0.81[EUR][1000 genomes]
rs3119591	0.81[EUR][1000 genomes]
rs3178839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795812	0.80[MEX][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs435776	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs449133	0.86[CEU][hapmap]
rs453569	0.80[EUR][1000 genomes]
rs4653945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs505629	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs536515	0.81[EUR][1000 genomes]
rs54108	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6656520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695278	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883748	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv873273	chr1:228450868-228556788	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv873274	chr1:228450868-228585837	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1798020	chr1:228456147-228556788	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	esv1818776	chr1:228456147-228556788	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv873275	chr1:228456147-228585837	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
14	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
15	nsv873276	chr1:228456943-228585837	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
17	esv1850422	chr1:228464248-228556788	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv468260	chr1:228464248-228556788	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv549294	chr1:228464248-228556788	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv873277	chr1:228464248-228556788	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv873278	chr1:228464248-228585837	Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
22	nsv468271	chr1:228464248-228601638	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
23	nsv468283	chr1:228464248-228601638	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
24	nsv468294	chr1:228464248-228601638	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
25	nsv549295	chr1:228464248-228601638	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
26	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
27	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
28	nsv873280	chr1:228500627-228603029	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
29	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
30	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
31	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
32	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653946	DUSP5P	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228510000-228554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228511400-228552400	Weak transcription	Psoas Muscle	Psoas
3	chr1:228527600-228546600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:228527600-228562400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:228527800-228555800	Weak transcription	Gastric	stomach
6	chr1:228530000-228547200	Weak transcription	Pancreas	Pancrea
7	chr1:228531200-228549600	Weak transcription	Esophagus	oesophagus
8	chr1:228531200-228551200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:228532400-228555200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:228532400-228562400	Weak transcription	Fetal Lung	lung
11	chr1:228533200-228548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:228535200-228554200	Weak transcription	Right Atrium	heart
13	chr1:228537000-228554800	Weak transcription	Fetal Intestine Large	intestine
14	chr1:228539400-228556000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:228539600-228548200	Weak transcription	Ovary	ovary
16	chr1:228540200-228546400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:228540400-228566200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:228541000-228565200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:228541000-228565400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:228541400-228562000	Weak transcription	Brain Germinal Matrix	brain
21	chr1:228541600-228562400	Weak transcription	Fetal Brain Female	brain
22	chr1:228541600-228565800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:228541800-228559800	Weak transcription	Lung	lung
24	chr1:228542200-228548200	Weak transcription	Fetal Intestine Small	intestine
25	chr1:228542800-228549800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:228542800-228555000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:228543400-228546600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:228544600-228549600	Weak transcription	Primary T cells from cord blood	blood
29	chr1:228545400-228546800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:228545800-228546400	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:228545800-228548600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:228545800-228562400	Weak transcription	HSMMtube	muscle
33	chr1:228546000-228546400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:228546000-228546400	Flanking Active TSS	Fetal Heart	heart
35	chr1:228546000-228546400	Weak transcription	Spleen	Spleen
36	chr1:228546000-228546600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:228546000-228547200	Weak transcription	Right Ventricle	heart
38	chr1:228546000-228549400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:228546000-228553600	Weak transcription	Left Ventricle	heart
40	chr1:228546200-228546400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:228546200-228546800	Bivalent Enhancer	HepG2	liver
42	chr1:228546200-228547200	ZNF genes & repeats	Fetal Stomach	stomach

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