Variant report

Variant	rs2240571
Chromosome Location	chr7:12609988-12609989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr7:12609769-12610291	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr7:12609606-12610156	MCF-7	breast:	n/a	chr7:12609886-12609897
3	E2F4	chr7:12609755-12610376	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr7:12609746-12610073	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr7:12609768-12610098	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr7:12609769-12610092	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr7:12609808-12610066	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF217	chr7:12609814-12610074	MCF-7	breast:	n/a	n/a
9	MAX	chr7:12609823-12611130	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr7:12609976-12610689	MCF-7	breast:	n/a	n/a
11	MYC	chr7:12609952-12610279	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr7:12609926-12610650	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr7:12609761-12610759	H1-neurons	neurons:	n/a	n/a
14	MAX	chr7:12609902-12611059	H1-hESC	embryonic stem cell:	n/a	n/a
15	HDAC2	chr7:12609765-12610671	MCF-7	breast:	n/a	n/a
16	E2F6	chr7:12609789-12611052	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr7:12609821-12610590	H1-hESC	embryonic stem cell:	n/a	n/a
18	STAT3	chr7:12609714-12610181	MCF10A-Er-Src	breast:	n/a	n/a
19	MAFK	chr7:12609778-12610080	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr7:12609884-12611114	H1-hESC	embryonic stem cell:	n/a	n/a
21	KAP1	chr7:12609878-12610532	U2OS	brain:	n/a	n/a
22	E2F6	chr7:12609691-12611074	H1-hESC	embryonic stem cell:	n/a	n/a
23	HA-E2F1	chr7:12609624-12610605	MCF-7	breast:	n/a	n/a
24	CEBPB	chr7:12609663-12610165	MCF-7	breast:	n/a	chr7:12609886-12609897
25	MYC	chr7:12609759-12610066	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr7:12609650-12610133	Hela-S3	cervix:	n/a	chr7:12609886-12609897
27	TEAD4	chr7:12609848-12610225	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAFK	chr7:12609768-12609990	HepG2	liver:	n/a	n/a
29	MAX	chr7:12609864-12610800	A549	lung:	n/a	n/a
30	SUZ12	chr7:12609858-12611660	NT2-D1	testis:	n/a	n/a
31	CEBPB	chr7:12609551-12610065	A549	lung:	n/a	chr7:12609886-12609897
32	POLR2A	chr7:12609948-12610150	H1-hESC	embryonic stem cell:	n/a	n/a
33	BACH1	chr7:12609643-12611073	H1-hESC	embryonic stem cell:	n/a	n/a
34	STAT3	chr7:12609808-12610063	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr7:12609903-12610278	MCF10A-Er-Src	breast:	n/a	n/a
36	MAX	chr7:12609950-12610684	A549	lung:	n/a	n/a
37	MAFK	chr7:12609775-12610037	HepG2	liver:	n/a	n/a
38	FOS	chr7:12609772-12610080	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr7:12609777-12610065	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

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

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWDE-1	chr7:12609751-12610474	ENSG00000225606.1

No data

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

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10233337	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10248988	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255606	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10276226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129315	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17283514	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17283696	0.95[JPT][hapmap]
rs1859989	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859990	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990223	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990224	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1990225	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2215063	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240574	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs2240575	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3173628	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3735221	0.88[EUR][1000 genomes]
rs3807863	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41379149	0.96[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs4361677	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55999874	0.81[AMR][1000 genomes]
rs6460965	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6460967	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460968	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6954111	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6954578	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6972418	0.80[EUR][1000 genomes]
rs6972477	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73060686	0.80[EUR][1000 genomes]
rs73293093	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7801351	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7811582	0.92[CEU][hapmap]
rs968792	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2240571	AC011891.5	cis	Thyroid	GTEx
rs2240571	SCIN	cis	parietal	SCAN
rs2240571	SCIN	cis	Thyroid	GTEx
rs2240571	SOSTDC1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12609400-12610000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:12609400-12610000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr7:12609400-12610000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr7:12609400-12610000	Bivalent Enhancer	Primary T cells from cord blood	blood
5	chr7:12609400-12610000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr7:12609400-12610000	Enhancers	Pancreas	Pancrea
7	chr7:12609400-12610000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr7:12609400-12610200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr7:12609400-12610200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:12609400-12610200	Bivalent Enhancer	Fetal Thymus	thymus
11	chr7:12609400-12610200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
12	chr7:12609400-12610200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr7:12609400-12610600	Active TSS	Hela-S3	cervix
14	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:12609400-12611000	Enhancers	Spleen	Spleen
16	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
17	chr7:12609400-12611600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr7:12609600-12610000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:12609600-12610000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:12609600-12610000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
21	chr7:12609600-12610000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr7:12609600-12610000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:12609600-12610000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr7:12609600-12610000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
25	chr7:12609600-12610000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:12609600-12610000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
27	chr7:12609600-12610000	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr7:12609600-12610000	Active TSS	Rectal Smooth Muscle	rectum
29	chr7:12609600-12610000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
30	chr7:12609600-12610000	Flanking Bivalent TSS/Enh	A549	lung
31	chr7:12609600-12610000	Flanking Active TSS	NHEK	skin
32	chr7:12609600-12610200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:12609600-12610200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:12609600-12610200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
35	chr7:12609600-12610200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
36	chr7:12609600-12610400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
37	chr7:12609600-12610400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:12609600-12610600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
39	chr7:12609600-12610600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:12609600-12610800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
41	chr7:12609600-12611000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
42	chr7:12609600-12611200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr7:12609600-12611200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr7:12609600-12611200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
45	chr7:12609600-12612000	Active TSS	Brain Anterior Caudate	brain
46	chr7:12609800-12610000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:12609800-12610000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:12609800-12610000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:12609800-12610000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr7:12609800-12610000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell

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