Variant report

Variant	rs12369491
Chromosome Location	chr12:11890508-11890509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11885204..11886814-chr12:11889100..11890983,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009951	0.92[CEU][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1009953	0.92[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1009954	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10743967	0.85[EUR][1000 genomes]
rs10845407	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10845408	0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10845410	0.85[AMR][1000 genomes]
rs11054429	0.81[EUR][1000 genomes]
rs11054433	0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs11054439	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11615175	0.88[CHD][hapmap]
rs12228191	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17818461	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17818498	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17818624	0.81[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2051525	0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2187641	0.88[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2187642	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2416882	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2416883	0.92[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2724599	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2724600	0.86[EUR][1000 genomes]
rs2724616	0.81[EUR][1000 genomes]
rs2724618	0.83[EUR][1000 genomes]
rs2724633	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724635	0.88[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs2724645	0.92[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724648	0.81[EUR][1000 genomes]
rs2856321	0.80[EUR][1000 genomes]
rs2856322	0.82[EUR][1000 genomes]
rs2856324	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2856338	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2856344	0.92[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2860431	0.88[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs2900208	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763719	0.92[CEU][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4763720	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763721	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488701	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs762717	0.92[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs972798	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11873400-11894200	Weak transcription	NHLF	lung
4	chr12:11880400-11896200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:11880600-11896400	Weak transcription	Fetal Stomach	stomach
6	chr12:11880800-11890800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:11883200-11894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:11883600-11891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:11883600-11891400	Weak transcription	Right Ventricle	heart
13	chr12:11883600-11894000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:11883600-11896200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:11883800-11906000	Weak transcription	Liver	Liver
16	chr12:11884000-11894000	Weak transcription	Right Atrium	heart
17	chr12:11884000-11894200	Weak transcription	Psoas Muscle	Psoas
18	chr12:11884200-11896200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:11884200-11899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:11884800-11893800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:11885200-11891400	Weak transcription	NHEK	skin
22	chr12:11885200-11891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:11885200-11894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:11885200-11894200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:11885200-11894200	Weak transcription	Osteobl	bone
26	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:11885400-11891400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:11885600-11892000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:11885600-11894200	Weak transcription	Esophagus	oesophagus
30	chr12:11885600-11898600	Weak transcription	Primary T cells from cord blood	blood
31	chr12:11885600-11899000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
33	chr12:11885800-11890600	Weak transcription	HUVEC	blood vessel
34	chr12:11885800-11893800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:11885800-11893800	Weak transcription	HMEC	breast
36	chr12:11885800-11894200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:11885800-11894200	Weak transcription	Gastric	stomach
38	chr12:11885800-11896800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:11885800-11898400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:11886000-11894200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:11886000-11900000	Weak transcription	Colonic Mucosa	Colon
43	chr12:11886200-11892400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:11886200-11892600	Genic enhancers	GM12878-XiMat	blood
45	chr12:11886600-11892400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:11886800-11892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:11886800-11897800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:11887000-11890800	Weak transcription	Thymus	Thymus
49	chr12:11887400-11894200	Weak transcription	Fetal Intestine Small	intestine
50	chr12:11887800-11896400	Weak transcription	Dnd41	blood

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