Variant report

Variant	rs10798391
Chromosome Location	chr1:171389938-171389939
allele	G/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	FOS	chr1:171389893-171390539	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108
2	STAT3	chr1:171389903-171390505	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107
3	FOSL1	chr1:171389800-171390429	HCT-116	colon:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108
4	STAT3	chr1:171389929-171390487	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107
5	SRF	chr1:171389919-171390463	MCF-7	breast:	n/a	chr1:171390339-171390353 chr1:171390341-171390354 chr1:171390339-171390357 chr1:171390342-171390353 chr1:171390343-171390357 chr1:171390342-171390359
6	STAT3	chr1:171389936-171390422	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107
7	FOS	chr1:171389925-171390422	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108
8	SRF	chr1:171389783-171390556	HCT-116	colon:	n/a	chr1:171390339-171390353 chr1:171390341-171390354 chr1:171390339-171390357 chr1:171390342-171390353 chr1:171390343-171390357 chr1:171390342-171390359
9	FOS	chr1:171389922-171390407	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108
10	POLR2A	chr1:171389900-171390375	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:171389921-171390555	MCF10A-Er-Src	breast:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108
12	SRF	chr1:171389786-171390663	HCT-116	colon:	n/a	chr1:171390339-171390353 chr1:171390341-171390354 chr1:171390339-171390357 chr1:171390342-171390353 chr1:171390343-171390357 chr1:171390342-171390359
13	JUND	chr1:171389905-171390398	H1-hESC	embryonic stem cell:	n/a	chr1:171390098-171390107 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390098-171390108 chr1:171390036-171390045 chr1:171390098-171390108

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171368098..171369611-chr1:171388402..171390157,2	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10912970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912984	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912990	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912991	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11809022	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12025678	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028255	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12031098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032556	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044181	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12564075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749160	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179880	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421812	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2901543	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34038212	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34350295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34643775	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34646870	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35025080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35247356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35680678	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7418672	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8179347	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171383200-171390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:171388000-171390800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:171388000-171391000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:171388400-171390200	Enhancers	Placenta	Placenta
5	chr1:171388600-171391200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:171388800-171390200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:171388800-171390400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:171388800-171391000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:171388800-171391400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:171388800-171394600	Enhancers	NHEK	skin
11	chr1:171389000-171390600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:171389000-171390800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:171389000-171391000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:171389000-171391400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:171389200-171391000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:171389200-171391800	Weak transcription	NHDF-Ad	bronchial
17	chr1:171389600-171390000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:171389600-171390000	Enhancers	Left Ventricle	heart
19	chr1:171389600-171390400	Enhancers	Primary T cells from cord blood	blood
20	chr1:171389600-171390400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:171389600-171390400	Enhancers	Stomach Mucosa	stomach
22	chr1:171389600-171390400	Enhancers	HMEC	breast
23	chr1:171389600-171390600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:171389600-171391200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:171389600-171391200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:171389600-171391400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:171389600-171391800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:171389600-171391800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:171389600-171394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:171389600-171394600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:171389800-171390000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr1:171389800-171390200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:171389800-171390400	Enhancers	GM12878-XiMat	blood
34	chr1:171389800-171390600	Enhancers	Adipose Nuclei	Adipose
35	chr1:171389800-171390800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr1:171389800-171390800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:171389800-171390800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:171389800-171391000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links