Variant report

Variant	rs7653521
Chromosome Location	chr3:93784559-93784560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:93770469..93772634-chr3:93784078..93786437,2	MCF-7	breast:
2	chr3:93739958..93742338-chr3:93782730..93785383,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10934892	0.84[EUR][1000 genomes]
rs12492553	0.92[EUR][1000 genomes]
rs12634349	0.82[JPT][hapmap]
rs13076476	0.84[ASW][hapmap]
rs13085785	1.00[CEU][hapmap]
rs1902105	0.82[EUR][1000 genomes]
rs2965	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34309901	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34411239	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35793773	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35815512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs4426680	0.86[EUR][1000 genomes]
rs4857146	0.92[EUR][1000 genomes]
rs4857186	0.88[EUR][1000 genomes]
rs56982991	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6123	0.83[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6764203	0.96[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs6765621	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777479	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs6791811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7633544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7637745	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7644769	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap]
rs8178610	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs8178616	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs921727	0.81[CEU][hapmap]
rs9844676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872376	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv967185	chr3:93771419-93794318	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
14	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7653521	OR5K2	cis	cerebellum	SCAN
rs7653521	ARL6	cis	cerebellum	SCAN
rs7653521	DHFRL1	cis	cerebellum	SCAN
rs7653521	WBP2NL	trans	cerebellum	SCAN
rs7653521	STX19	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782400-93804400	Weak transcription	Spleen	Spleen
2	chr3:93782600-93786800	Enhancers	Stomach Mucosa	stomach
3	chr3:93782800-93784600	Enhancers	Fetal Brain Male	brain
4	chr3:93782800-93785000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:93782800-93785200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:93782800-93785200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:93782800-93785200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:93782800-93785600	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:93782800-93785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:93782800-93785800	Weak transcription	Fetal Kidney	kidney
11	chr3:93782800-93792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:93782800-93795200	Weak transcription	HSMMtube	muscle
13	chr3:93782800-93795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:93782800-93799200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:93782800-93799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:93782800-93813400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:93783000-93784600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:93783000-93785000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:93783000-93785200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:93783000-93785400	Weak transcription	Fetal Lung	lung
23	chr3:93783000-93785400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:93783000-93785600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:93783000-93785600	Weak transcription	Placenta	Placenta
26	chr3:93783000-93785600	Weak transcription	Fetal Stomach	stomach
27	chr3:93783000-93785800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:93783000-93785800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:93783000-93785800	Weak transcription	Left Ventricle	heart
30	chr3:93783000-93785800	Weak transcription	Thymus	Thymus
31	chr3:93783000-93786600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:93783000-93790400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:93783000-93790600	Weak transcription	Esophagus	oesophagus
34	chr3:93783000-93790600	Weak transcription	Gastric	stomach
35	chr3:93783000-93790600	Weak transcription	Lung	lung
36	chr3:93783000-93790600	Weak transcription	Pancreas	Pancrea
37	chr3:93783000-93795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:93783000-93795000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:93783000-93795200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:93783000-93795200	Weak transcription	NH-A	brain
41	chr3:93783000-93803000	Weak transcription	Psoas Muscle	Psoas
42	chr3:93783000-93810600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:93783000-93813800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:93783000-93813800	Weak transcription	Right Ventricle	heart
45	chr3:93783200-93785800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:93783200-93786000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:93783200-93824600	Weak transcription	NHEK	skin
48	chr3:93783200-93851600	Weak transcription	HMEC	breast
49	chr3:93783400-93784600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:93783400-93784800	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links