Variant report

Variant	rs10946208
Chromosome Location	chr6:167459596-167459597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167459004..167459905-chr6:167555024..167555917,3	MCF-7	breast:
2	chr6:167453011..167457183-chr6:167458189..167461851,4	K562	blood:
3	chr6:167200327..167200836-chr6:167459295..167459843,2	K562	blood:
4	chr6:167188018..167188945-chr6:167458801..167459761,3	MCF-7	breast:

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10455982	0.87[AMR][1000 genomes]
rs10484530	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10484531	0.89[AMR][1000 genomes]
rs1060404	0.87[AMR][1000 genomes]
rs10946203	0.87[AMR][1000 genomes]
rs10946204	0.87[AMR][1000 genomes]
rs10946205	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10946207	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12178491	0.83[EUR][1000 genomes]
rs12193698	0.80[EUR][1000 genomes]
rs12203510	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208359	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12209395	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12212247	0.87[AMR][1000 genomes]
rs12213683	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523712	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526548	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12527827	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528323	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528689	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529238	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529876	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529959	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195812	0.82[AMR][1000 genomes]
rs13204839	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13208636	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210649	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13213249	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1322077	0.84[AMR][1000 genomes]
rs1358882	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358883	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407315	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524252	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17615336	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1810644	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810645	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1894603	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001114	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001115	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017338	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2038580	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2181058	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181059	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236313	0.81[JPT][hapmap]
rs2237272	0.87[AMR][1000 genomes]
rs2237273	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2237274	0.86[JPT][hapmap]
rs2237276	0.81[AMR][1000 genomes]
rs2237277	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2239823	0.80[EUR][1000 genomes]
rs2239826	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2239827	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282860	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2282861	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2285147	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285148	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2301436	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239933	0.80[AMR][1000 genomes]
rs35171809	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3752520	0.87[AMR][1000 genomes]
rs4710171	0.87[AMR][1000 genomes]
rs4710175	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4710176	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62436765	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456143	0.82[AMR][1000 genomes]
rs6456146	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6456149	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456150	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456151	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456152	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6456153	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456154	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902119	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904946	0.82[AMR][1000 genomes]
rs6909180	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909475	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909502	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918286	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920858	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6921588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6923582	0.82[AMR][1000 genomes]
rs6925969	0.83[EUR][1000 genomes]
rs6929466	0.81[AMR][1000 genomes]
rs6932740	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934043	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936261	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6941355	0.86[EUR][1000 genomes]
rs720325	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742305	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748224	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749278	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7760495	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761977	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762156	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766242	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs911632	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916331	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9295384	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295385	0.82[AMR][1000 genomes]
rs9457249	0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs9457251	0.83[AMR][1000 genomes]
rs9457252	0.87[AMR][1000 genomes]
rs9457254	0.84[AMR][1000 genomes]
rs9457256	0.87[AMR][1000 genomes]
rs9457257	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9457258	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9457259	0.86[AMR][1000 genomes]
rs9457260	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9457261	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457268	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9457270	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9459835	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs9459836	0.87[AMR][1000 genomes]
rs9459838	0.86[AMR][1000 genomes]
rs9459839	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9459840	0.82[AMR][1000 genomes]
rs9459841	0.82[AMR][1000 genomes]
rs9459842	0.82[AMR][1000 genomes]
rs9459845	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9459846	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9459849	0.87[AMR][1000 genomes]
rs9459853	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9459854	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9459855	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9459862	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9459871	0.86[EUR][1000 genomes]
rs9459872	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9459874	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
7	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
9	nsv464140	chr6:167426681-167492552	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv886943	chr6:167440244-167502638	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2752099	chr6:167448181-167579102	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv519550	chr6:167450609-167473685	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv1841903	chr6:167459596-167489090	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10946208	RNASET2	cis	Whole Blood	GTEx
rs10946208	AL133458.1	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167441000-167461800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:167441400-167473400	Weak transcription	Psoas Muscle	Psoas
3	chr6:167445600-167460200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:167448200-167459800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:167448200-167467200	Weak transcription	HMEC	breast
6	chr6:167448400-167467200	Weak transcription	NHEK	skin
7	chr6:167448800-167460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:167449000-167467800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:167449000-167470400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:167449800-167459600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:167449800-167462800	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:167450000-167460800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:167450000-167467400	Weak transcription	Ovary	ovary
14	chr6:167450200-167463000	Weak transcription	Brain Germinal Matrix	brain
15	chr6:167450600-167460600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:167450600-167463000	Weak transcription	Fetal Brain Female	brain
17	chr6:167451200-167460200	Weak transcription	Placenta	Placenta
18	chr6:167451600-167461600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:167451600-167462000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:167451600-167463600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:167451600-167467000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:167451600-167467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:167451600-167468400	Weak transcription	Esophagus	oesophagus
24	chr6:167452000-167460000	Weak transcription	Stomach Mucosa	stomach
25	chr6:167453800-167460200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:167454000-167460200	Weak transcription	Fetal Thymus	thymus
27	chr6:167454000-167460200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:167454000-167463400	Weak transcription	Aorta	Aorta
29	chr6:167454000-167464600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:167454200-167459600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:167454200-167459800	Weak transcription	Fetal Lung	lung
32	chr6:167454200-167462600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:167454400-167461600	Weak transcription	A549	lung
34	chr6:167454400-167463200	Weak transcription	Brain Substantia Nigra	brain
35	chr6:167454600-167464400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:167454800-167459800	Strong transcription	Fetal Intestine Small	intestine
37	chr6:167455000-167459800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:167455000-167462600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:167455000-167462800	Weak transcription	HSMM	muscle
40	chr6:167455000-167470600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:167455200-167467600	Weak transcription	Liver	Liver
42	chr6:167455400-167459600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:167455400-167459800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr6:167456000-167460400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:167456200-167459600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:167456200-167460600	Weak transcription	Adipose Nuclei	Adipose
47	chr6:167456200-167467000	Weak transcription	Left Ventricle	heart
48	chr6:167456200-167467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:167456200-167468400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:167456200-167470800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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