Variant report

Variant	rs10934164
Chromosome Location	chr3:112012692-112012693
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	chr3:112011328..112014210-chr3:112359098..112361496,2	MCF-7	breast:
2	chr3:112012262..112013019-chr3:112156556..112157096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10511310	1.00[CHB][hapmap]
rs10804498	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934163	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10934165	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	1.00[ASN][1000 genomes]
rs11926389	1.00[CHB][hapmap]
rs12489470	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12636943	1.00[CHB][hapmap]
rs13063452	1.00[CHB][hapmap]
rs13064242	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084897	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13092220	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1317295	1.00[ASN][1000 genomes]
rs1317658	1.00[ASN][1000 genomes]
rs13316383	1.00[ASN][1000 genomes]
rs1388858	1.00[CHB][hapmap]
rs1388859	1.00[CHB][hapmap]
rs1492479	1.00[ASN][1000 genomes]
rs1492489	1.00[CHB][hapmap]
rs17446282	1.00[CHB][hapmap]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	1.00[ASN][1000 genomes]
rs4234409	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs4234411	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs4434123	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs4507229	1.00[ASN][1000 genomes]
rs4538347	1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	1.00[CHB][hapmap]
rs4682393	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682400	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	1.00[ASN][1000 genomes]
rs56008438	1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	1.00[ASN][1000 genomes]
rs62278768	1.00[ASN][1000 genomes]
rs62278769	1.00[ASN][1000 genomes]
rs62278770	1.00[ASN][1000 genomes]
rs62278771	1.00[ASN][1000 genomes]
rs62278843	1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6764824	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6774756	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6781844	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs6787323	1.00[CHB][hapmap]
rs6789875	1.00[CHB][hapmap]
rs6795820	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6797177	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs6801795	1.00[CHB][hapmap]
rs6804836	1.00[CHB][hapmap]
rs6805112	1.00[CHB][hapmap]
rs6805397	1.00[CHB][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs732686	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7609904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7612748	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7615460	1.00[CHB][hapmap]
rs7621431	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7625249	1.00[CHB][hapmap]
rs7631673	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7636107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7637682	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9288939	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs9288942	0.87[ASW][hapmap];1.00[CHB][hapmap]
rs9810170	1.00[CHB][hapmap]
rs9810421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816969	1.00[ASN][1000 genomes]
rs9818407	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	1.00[ASN][1000 genomes]
rs9851141	0.81[AMR][1000 genomes]
rs9851760	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9853669	1.00[ASN][1000 genomes]
rs9855755	1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised 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	8 gene(s)	inside rSNPs	diseases
2	nsv877340	chr3:111936961-112013546	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10934164	CD200	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112012200-112012800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr3:112012200-112012800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:112012200-112013000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:112012200-112013200	Active TSS	Colon Smooth Muscle	Colon
5	chr3:112012200-112013200	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr3:112012200-112013200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:112012200-112013200	Active TSS	Fetal Kidney	kidney
8	chr3:112012200-112013200	Flanking Active TSS	GM12878-XiMat	blood
9	chr3:112012200-112013200	Active TSS	NHDF-Ad	bronchial
10	chr3:112012200-112013400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:112012200-112013400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:112012400-112012800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:112012400-112012800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:112012400-112012800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:112012400-112012800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:112012400-112012800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:112012400-112012800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr3:112012400-112012800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr3:112012400-112012800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:112012400-112012800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:112012400-112012800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr3:112012400-112012800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:112012400-112012800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:112012400-112012800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr3:112012400-112012800	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr3:112012400-112012800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr3:112012400-112012800	Flanking Active TSS	Fetal Lung	lung
28	chr3:112012400-112012800	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr3:112012400-112012800	Flanking Active TSS	HepG2	liver
30	chr3:112012400-112012800	Flanking Active TSS	NHEK	skin
31	chr3:112012400-112012800	Flanking Active TSS	NHLF	lung
32	chr3:112012400-112013000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:112012400-112013000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:112012400-112013000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:112012400-112013000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:112012400-112013000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr3:112012400-112013000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:112012400-112013000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:112012400-112013000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:112012400-112013000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr3:112012400-112013000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr3:112012400-112013000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:112012400-112013000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:112012400-112013000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:112012400-112013000	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:112012400-112013000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:112012400-112013000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:112012400-112013000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:112012400-112013000	Enhancers	Fetal Heart	heart
50	chr3:112012400-112013000	Active TSS	Fetal Intestine Large	intestine

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