Variant report

Variant	rs752107
Chromosome Location	chr1:228247351-228247352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228242970..228244835-chr1:228244981..228247673,2	MCF-7	breast:
2	chr1:228193180..228197909-chr1:228245616..228249822,4	MCF-7	breast:
3	chr1:228245943..228247915-chr1:228251913..228254649,3	K562	blood:
4	chr1:228244560..228247525-chr1:228272017..228274884,2	MCF-7	breast:
5	chr1:228246811..228249127-chr1:228257869..228259965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12084338	0.82[ASW][hapmap]
rs12130630	0.92[YRI][hapmap]
rs12134624	0.82[ASW][hapmap];0.83[GIH][hapmap];0.92[YRI][hapmap]
rs1557026	1.00[YRI][hapmap]
rs1745423	0.80[TSI][hapmap]
rs28634124	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3094911	0.83[ASW][hapmap]
rs3121310	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs3845621	0.84[YRI][hapmap]
rs4653917	0.82[ASW][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs4653921	1.00[YRI][hapmap]
rs6426492	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs6657968	1.00[YRI][hapmap]
rs6673893	1.00[YRI][hapmap]
rs6682260	0.82[ASW][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs6704220	0.90[YRI][hapmap]
rs708123	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs708124	0.92[ASW][hapmap]
rs7523917	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539762	0.82[ASW][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs766972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822725	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822739	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822740	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs849749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9728319	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	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
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	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
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	esv1814215	chr1:228231601-228259932	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
10	esv1844252	chr1:228231601-228259932	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
12	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
13	nsv826964	chr1:228246802-228247654	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs752107	GUK1	cis	parietal	SCAN
rs752107	ITPKB	cis	cerebellum	SCAN
rs752107	TMEM63A	cis	cerebellum	SCAN
rs752107	MRPL55	cis	cerebellum	SCAN
rs752107	C1orf69	cis	cerebellum	SCAN
rs752107	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs752107	WDR26	cis	cerebellum	SCAN
rs752107	OBSCN	cis	Esophagus Mucosa	GTEx
rs752107	ACBD3	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228246200-228248800	ZNF genes & repeats	Spleen	Spleen
2	chr1:228246400-228247600	Bivalent Enhancer	Placenta	Placenta
3	chr1:228246400-228248200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:228246600-228247400	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr1:228246600-228247400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:228246600-228247600	Bivalent Enhancer	Stomach Mucosa	stomach
7	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
8	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:228246600-228248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:228246600-228249000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:228246600-228249000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:228246600-228249000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:228246600-228249000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:228246800-228247400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:228246800-228247400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
17	chr1:228246800-228247400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:228246800-228247400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:228246800-228247400	Bivalent/Poised TSS	Thymus	Thymus
20	chr1:228246800-228247600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr1:228246800-228247600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:228246800-228247600	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr1:228246800-228247800	Bivalent Enhancer	Fetal Heart	heart
24	chr1:228246800-228248000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
25	chr1:228246800-228248000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr1:228246800-228248000	Bivalent/Poised TSS	NHEK	skin
27	chr1:228246800-228248200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:228246800-228248600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr1:228246800-228249000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr1:228247000-228247400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
31	chr1:228247000-228247600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:228247000-228247600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
33	chr1:228247000-228247600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
34	chr1:228247000-228247800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:228247000-228247800	Bivalent Enhancer	Brain Hippocampus Middle	brain
36	chr1:228247000-228247800	Bivalent/Poised TSS	Colonic Mucosa	Colon
37	chr1:228247000-228247800	Bivalent Enhancer	Fetal Brain Male	brain
38	chr1:228247000-228247800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
39	chr1:228247000-228248000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr1:228247000-228248000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
41	chr1:228247000-228248200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
42	chr1:228247000-228248200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr1:228247000-228248200	Bivalent/Poised TSS	Esophagus	oesophagus
44	chr1:228247000-228248200	Bivalent/Poised TSS	Fetal Brain Female	brain
45	chr1:228247000-228248200	Bivalent Enhancer	Ovary	ovary
46	chr1:228247000-228248200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
47	chr1:228247000-228248400	Bivalent Enhancer	Fetal Thymus	thymus
48	chr1:228247000-228248400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
49	chr1:228247000-228248600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
50	chr1:228247000-228248600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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