Variant report

Variant	rs3735222
Chromosome Location	chr7:12609679-12609680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:12609606-12610156	MCF-7	breast:	n/a	chr7:12609886-12609897
2	BACH1	chr7:12609596-12609730	K562	blood:	n/a	n/a
3	CEBPB	chr7:12609535-12609983	H1-hESC	embryonic stem cell:	n/a	chr7:12609886-12609897
4	HA-E2F1	chr7:12609624-12610605	MCF-7	breast:	n/a	n/a
5	CEBPB	chr7:12609663-12610165	MCF-7	breast:	n/a	chr7:12609886-12609897
6	CEBPB	chr7:12609650-12610133	Hela-S3	cervix:	n/a	chr7:12609886-12609897
7	CEBPB	chr7:12609674-12609918	K562	blood:	n/a	chr7:12609886-12609897
8	CEBPB	chr7:12609551-12610065	A549	lung:	n/a	chr7:12609886-12609897
9	BACH1	chr7:12609643-12611073	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12602342..12604561-chr7:12608286..12609928,3	K562	blood:
2	chr7:12608764..12610772-chr7:12727255..12728888,2	K562	blood:
3	chr7:12602342..12605416-chr7:12608401..12610045,3	K562	blood:

Variant related genes	Relation type
SCIN	TF binding region
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1034856	0.92[CEU][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1118998	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11558844	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11973033	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17283696	0.82[CEU][hapmap]
rs17283717	0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17355921	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1990224	0.92[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1990225	0.92[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs2240572	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240574	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3735223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41356146	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41379149	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4458754	0.92[CEU][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55682719	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55829483	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55999874	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56085455	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56274604	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56760264	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57710906	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57778115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57805173	0.84[AMR][1000 genomes]
rs6460964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460965	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6954111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6961909	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6965970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967031	0.82[GIH][hapmap];0.94[JPT][hapmap]
rs6972418	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73060662	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73060664	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73060678	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73060679	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73060680	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73060684	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73060686	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73062610	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73062611	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73062639	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7782451	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799976	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7803810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804260	0.92[CEU][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7811582	0.84[ASW][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528031	chr7:12536336-12618764	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1025397	chr7:12543161-12612059	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1025006	chr7:12543161-12618924	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027831	chr7:12543161-12619740	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv470066	chr7:12543794-12618764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033478	chr7:12547121-12618924	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv464379	chr7:12572742-12618764	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv606231	chr7:12572742-12618764	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3735222	SCIN	Cis_1M	lymphoblastoid	RTeQTL
rs3735222	SOSTDC1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12597200-12609800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:12598400-12609800	Weak transcription	Placenta	Placenta
3	chr7:12608600-12609800	Weak transcription	K562	blood
4	chr7:12609200-12609800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:12609400-12609800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
6	chr7:12609400-12609800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr7:12609400-12609800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr7:12609400-12609800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:12609400-12609800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:12609400-12609800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:12609400-12609800	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr7:12609400-12609800	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr7:12609400-12609800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr7:12609400-12609800	Enhancers	HMEC	breast
15	chr7:12609400-12609800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
16	chr7:12609400-12610000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:12609400-12610000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr7:12609400-12610000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr7:12609400-12610000	Bivalent Enhancer	Primary T cells from cord blood	blood
20	chr7:12609400-12610000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr7:12609400-12610000	Enhancers	Pancreas	Pancrea
22	chr7:12609400-12610000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr7:12609400-12610200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr7:12609400-12610200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:12609400-12610200	Bivalent Enhancer	Fetal Thymus	thymus
26	chr7:12609400-12610200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
27	chr7:12609400-12610200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr7:12609400-12610600	Active TSS	Hela-S3	cervix
29	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:12609400-12611000	Enhancers	Spleen	Spleen
31	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
32	chr7:12609400-12611600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr7:12609600-12609800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr7:12609600-12609800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr7:12609600-12609800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr7:12609600-12609800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:12609600-12609800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr7:12609600-12609800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr7:12609600-12609800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:12609600-12609800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr7:12609600-12609800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:12609600-12609800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:12609600-12609800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
44	chr7:12609600-12609800	Bivalent Enhancer	Brain Substantia Nigra	brain
45	chr7:12609600-12609800	Flanking Active TSS	Colonic Mucosa	Colon
46	chr7:12609600-12609800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
47	chr7:12609600-12609800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
48	chr7:12609600-12609800	Flanking Active TSS	Stomach Mucosa	stomach
49	chr7:12609600-12609800	Bivalent Enhancer	HUVEC	blood vessel
50	chr7:12609600-12609800	Bivalent/Poised TSS	NH-A	brain

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