Variant report

Variant	rs2357391
Chromosome Location	chr2:10061592-10061593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10054070..10056636-chr2:10061535..10064977,4	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1022312	0.92[MEX][hapmap]
rs10495576	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1054561	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1054565	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10803706	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10803707	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803708	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10803709	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803710	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929620	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929621	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10929624	0.82[JPT][hapmap]
rs11677649	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11686239	0.92[MEX][hapmap]
rs12185678	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12185679	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12185707	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12464092	0.84[ASN][1000 genomes]
rs12465661	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12467598	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468764	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12471962	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473944	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12479251	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12614753	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12615461	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617033	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621371	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12623211	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623217	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624026	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12991487	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991584	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12995394	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13000106	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13008907	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025784	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1367385	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16867226	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16867233	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16867239	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16867240	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1820965	0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1820966	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1820967	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1835426	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241665	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303921	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2357390	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2884175	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34577787	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35609983	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36009173	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs372222	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3815977	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs392617	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs394308	0.84[ASN][1000 genomes]
rs409920	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs417271	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs421030	1.00[YRI][hapmap]
rs445742	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs450085	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs450192	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668650	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668653	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669487	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669489	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669490	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669491	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669492	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669493	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669497	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669500	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514905	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55664551	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564933	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs565683	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58979565	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127468	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432041	0.91[MEX][hapmap]
rs6707887	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721644	0.82[JPT][hapmap]
rs6742427	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9750736	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2357391	TAF1B	cis	cerebellum	SCAN
rs2357391	TAF1B	cis	parietal	SCAN
rs2357391	NTSR2	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
3	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
5	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:10044200-10065200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
16	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:10047200-10061600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
19	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
20	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
21	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:10049600-10065200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:10051200-10064400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:10053200-10077800	Weak transcription	Liver	Liver
27	chr2:10054600-10073400	Weak transcription	Brain Substantia Nigra	brain
28	chr2:10054800-10063600	Weak transcription	Small Intestine	intestine
29	chr2:10054800-10065000	Weak transcription	Lung	lung
30	chr2:10054800-10066000	Weak transcription	Fetal Brain Male	brain
31	chr2:10054800-10069200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:10054800-10072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
34	chr2:10055000-10064000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:10055000-10064800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:10055000-10067600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:10055000-10072600	Weak transcription	Spleen	Spleen
38	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
39	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:10055200-10063400	Weak transcription	Hela-S3	cervix
42	chr2:10055200-10072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:10055200-10072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:10055200-10073200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:10055200-10079600	Weak transcription	K562	blood
46	chr2:10055200-10080800	Weak transcription	HMEC	breast
47	chr2:10055600-10073000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:10055800-10075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:10056400-10063800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:10056600-10064000	Weak transcription	Fetal Brain Female	brain

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