Variant report

Variant	rs2160010
Chromosome Location	chr7:120688463-120688464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr7:120688168-120688506	K562	blood:	n/a	n/a
2	ZC3H11A	chr7:120688360-120688467	K562	blood:	n/a	n/a
3	RCOR1	chr7:120688341-120688464	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:120687520..120689259-chr7:120697389..120698977,2	K562	blood:
2	chr7:120659278..120662150-chr7:120687240..120689583,2	K562	blood:
3	chr7:120688120..120689909-chr7:120713674..120716576,3	K562	blood:
4	chr7:120685095..120691151-chr7:120712234..120720635,10	K562	blood:
5	chr7:120688105..120689645-chr7:120709795..120712085,2	K562	blood:

No data

Variant related genes	Relation type
HMGN1P18	TF binding region
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10085563	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233922	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12706310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986767	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013087	0.84[CEU][hapmap]
rs2074577	0.85[CEU][hapmap]
rs2110276	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2160011	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160012	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2538485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538487	1.00[ASN][1000 genomes]
rs2721325	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721345	1.00[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896299	0.84[CEU][hapmap]
rs2908570	0.99[ASN][1000 genomes]
rs41688	0.85[CEU][hapmap]
rs4727915	0.84[CEU][hapmap]
rs4727917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730985	0.83[CEU][hapmap]
rs4730988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730991	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965415	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808535	0.84[CEU][hapmap]
rs7808593	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1031282	chr7:120667937-120887301	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv539099	chr7:120667937-120887301	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019025	chr7:120667937-120918696	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv539100	chr7:120667937-120918696	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv534342	chr7:120667938-120887300	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv889118	chr7:120683751-120800837	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv889119	chr7:120688463-120800837	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160010	FLJ21986	cis	multi-tissue	Pritchard
rs2160010	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120673400-120689200	Weak transcription	HSMMtube	muscle
2	chr7:120673800-120694200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:120682000-120689200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:120682000-120689400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:120682000-120689400	Weak transcription	Osteobl	bone
6	chr7:120682200-120695800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:120682400-120719600	Weak transcription	Fetal Lung	lung
8	chr7:120682600-120692000	Weak transcription	Fetal Stomach	stomach
9	chr7:120682800-120700800	Weak transcription	Fetal Kidney	kidney
10	chr7:120683200-120689400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:120683200-120689400	Weak transcription	Right Ventricle	heart
12	chr7:120683800-120689400	Weak transcription	Ovary	ovary
13	chr7:120683800-120689400	Weak transcription	Psoas Muscle	Psoas
14	chr7:120683800-120690800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:120684000-120694000	Weak transcription	Small Intestine	intestine
16	chr7:120684200-120689400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:120684400-120689200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:120684400-120689200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:120684400-120689400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:120684400-120689400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:120684400-120689600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:120685000-120689600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:120685600-120690000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr7:120686800-120690000	Weak transcription	Placenta	Placenta
25	chr7:120687000-120689600	Strong transcription	Adipose Nuclei	Adipose
26	chr7:120687000-120689800	Strong transcription	HSMM	muscle
27	chr7:120687200-120688600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:120687400-120689400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:120687400-120689400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:120687600-120689200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:120687600-120689400	Weak transcription	Hela-S3	cervix
32	chr7:120687800-120689200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:120687800-120689400	Strong transcription	Left Ventricle	heart
34	chr7:120687800-120689800	Strong transcription	NHLF	lung
35	chr7:120687800-120706600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:120688000-120688600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:120688000-120688600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:120688000-120689000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:120688000-120690200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr7:120688200-120689000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr7:120688400-120689000	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:120688400-120689000	Genic enhancers	K562	blood
43	chr7:120688400-120689200	Weak transcription	Liver	Liver
44	chr7:120688400-120689200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr7:120688400-120690000	Weak transcription	NHDF-Ad	bronchial
46	chr7:120688400-120690800	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links