Variant report

Variant	rs2179881
Chromosome Location	chr1:171390830-171390831
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	USF1	chr1:171390656-171390835	SK-N-SH_RA	brain:	n/a	n/a
2	USF1	chr1:171390449-171391114	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF2	chr1:171390609-171390912	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF1	chr1:171390620-171390934	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RNU6-290P	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12061485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12145071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12401720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12410247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2223894	0.89[AFR][1000 genomes]
rs2223895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696937	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv470745	chr1:171381746-171409514	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv465628	chr1:171381746-171409515	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv548189	chr1:171381746-171409515	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171388000-171391000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:171388600-171391200	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr1:171388800-171391000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:171388800-171391400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:171388800-171394600	Enhancers	NHEK	skin
6	chr1:171389000-171391000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:171389000-171391400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:171389200-171391000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:171389200-171391800	Weak transcription	NHDF-Ad	bronchial
10	chr1:171389600-171391200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:171389600-171391200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:171389600-171391400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:171389600-171391800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:171389600-171391800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:171389600-171394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:171389600-171394600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:171389800-171391000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:171390000-171391400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:171390200-171391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:171390200-171391000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:171390200-171392000	Enhancers	HUVEC	blood vessel
22	chr1:171390400-171391200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:171390400-171391800	Weak transcription	HMEC	breast
24	chr1:171390600-171391000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr1:171390600-171391600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:171390600-171391600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:171390600-171392800	Enhancers	NHLF	lung
28	chr1:171390600-171393600	Enhancers	Placenta	Placenta
29	chr1:171390800-171391200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:171390800-171391200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:171390800-171391800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:171390800-171393000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:171390800-171398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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