Variant report

Variant	rs11174417
Chromosome Location	chr12:62691335-62691336
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	chr12:62688856..62691778-chr12:62700983..62703361,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10160868	0.87[YRI][hapmap]
rs10160955	0.82[CHD][hapmap];0.95[LWK][hapmap];0.88[YRI][hapmap]
rs10431509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459253	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10506440	0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10747958	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784292	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10877819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10877820	0.93[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10877824	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877826	0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10877829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877831	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877834	0.88[YRI][hapmap]
rs11174397	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs11174398	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs11174399	0.82[AFR][1000 genomes]
rs11174401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174404	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174408	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174409	0.87[ASN][1000 genomes]
rs11174410	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11174411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174416	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174418	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11174420	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174423	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174424	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174431	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11174433	0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174435	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174436	0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11174437	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11174438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11174449	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11174458	0.84[YRI][hapmap]
rs11504121	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11504122	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11561463	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836268	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12228015	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229271	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12231778	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297474	0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12299072	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12306066	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12307900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308455	0.91[YRI][hapmap]
rs12310318	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310616	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310651	0.82[CHD][hapmap];0.95[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12311259	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12311279	0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12315645	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12317437	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12318287	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12424732	0.86[MKK][hapmap]
rs1376342	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1496859	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1901239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131435	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2132651	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2167287	0.80[CHD][hapmap];0.95[LWK][hapmap];0.88[YRI][hapmap]
rs2242032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28526400	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35634758	0.87[ASN][1000 genomes]
rs3803106	0.82[CHD][hapmap];0.95[LWK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6581444	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67044039	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67853252	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7132814	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133294	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137068	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295013	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7298827	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7300928	0.82[CHD][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7302033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302617	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73321563	0.84[AFR][1000 genomes]
rs767391	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs7953967	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956332	0.84[AFR][1000 genomes]
rs7963950	0.82[CHD][hapmap];0.95[LWK][hapmap];0.88[YRI][hapmap]
rs7965326	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974973	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7976058	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976608	0.84[YRI][hapmap]
rs902971	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9634284	0.88[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62679400-62696800	Weak transcription	Fetal Brain Male	brain
2	chr12:62683600-62697600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:62684000-62716200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:62686200-62720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:62686400-62698200	Weak transcription	Small Intestine	intestine
6	chr12:62686400-62736400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:62686600-62696600	Weak transcription	NH-A	brain
8	chr12:62686800-62697000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:62686800-62698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:62686800-62704600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:62687000-62693000	Weak transcription	Fetal Heart	heart
12	chr12:62687000-62695800	Strong transcription	Dnd41	blood
13	chr12:62687000-62696600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:62687000-62696800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:62687000-62697200	Weak transcription	NHLF	lung
16	chr12:62687000-62698200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:62687000-62699600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:62687000-62701400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:62687000-62702000	Weak transcription	Gastric	stomach
20	chr12:62687200-62718200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:62687400-62720600	Weak transcription	Right Ventricle	heart
22	chr12:62687600-62693400	Strong transcription	Fetal Lung	lung
23	chr12:62687800-62693200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:62687800-62693400	Strong transcription	Fetal Thymus	thymus
25	chr12:62688000-62691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:62688000-62691400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:62688000-62691400	Strong transcription	NHDF-Ad	bronchial
28	chr12:62688000-62691600	Strong transcription	HMEC	breast
29	chr12:62688000-62692000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:62688000-62692000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:62688000-62693000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr12:62688000-62693200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:62688000-62693400	Strong transcription	Liver	Liver
34	chr12:62688400-62691400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:62688400-62691600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr12:62688400-62693200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:62688600-62691400	Strong transcription	HepG2	liver
38	chr12:62688600-62691400	Strong transcription	HSMM	muscle
39	chr12:62688600-62691600	Strong transcription	Brain Anterior Caudate	brain
40	chr12:62688600-62691600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:62688600-62691600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:62688600-62692000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:62688600-62692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:62688600-62692200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:62688600-62692200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:62688600-62692400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:62688600-62692600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:62688600-62692800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:62688600-62692800	Strong transcription	Osteobl	bone
50	chr12:62688600-62693000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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