Variant report

Variant	rs7636107
Chromosome Location	chr3:112015292-112015293
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	chr3:112003335..112004963-chr3:112013883..112016627,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10511310	1.00[CHB][hapmap]
rs10804498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934164	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]
rs10934165	1.00[AFR][1000 genomes];0.97[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	1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12636943	1.00[CHB][hapmap]
rs13063452	1.00[CHB][hapmap]
rs13064242	1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084897	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13092220	0.88[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	1.00[CHB][hapmap]
rs4234411	1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	1.00[CHB][hapmap]
rs4434123	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	0.89[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	0.96[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	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6774756	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6781844	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	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]
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];1.00[ASN][1000 genomes]
rs7625249	1.00[CHB][hapmap]
rs7631673	1.00[ASN][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7637682	1.00[CHB][hapmap]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9288939	1.00[CHB][hapmap]
rs9288942	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]
rs9851760	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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs7636107	CD200	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112012800-112015800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:112012800-112015800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:112012800-112017600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:112013000-112016000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:112013000-112016200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:112013000-112016200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:112013000-112016200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:112013000-112021400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112013200-112015600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:112013200-112015800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:112013200-112015800	Weak transcription	Primary T cells from cord blood	blood
12	chr3:112013200-112015800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:112013200-112015800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:112013200-112016200	Weak transcription	Fetal Brain Male	brain
15	chr3:112013200-112017400	Weak transcription	Fetal Thymus	thymus
16	chr3:112013200-112020200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:112013200-112021000	Weak transcription	Thymus	Thymus
18	chr3:112013200-112021400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:112013400-112015600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:112013400-112015800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:112013400-112015800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:112013400-112015800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:112013400-112016000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:112013400-112016200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:112013400-112016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:112013400-112016200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:112013400-112021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:112013400-112022200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:112013800-112016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:112014200-112015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:112014600-112015800	Enhancers	GM12878-XiMat	blood

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