Variant report

Variant	rs6771309
Chromosome Location	chr3:111343919-111343920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11914473	1.00[ASN][1000 genomes]
rs1513328	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16858327	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs16858329	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16858353	0.88[CHD][hapmap]
rs2895386	0.99[ASN][1000 genomes]
rs3733176	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56172864	1.00[ASN][1000 genomes]
rs56306480	1.00[ASN][1000 genomes]
rs57067927	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57501419	0.98[ASN][1000 genomes]
rs57831621	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763322	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765832	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768092	1.00[ASN][1000 genomes]
rs6770144	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770679	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780729	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787870	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801876	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230132	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230143	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73852844	1.00[ASN][1000 genomes]
rs73852849	1.00[ASN][1000 genomes]
rs7431849	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637536	0.88[ASN][1000 genomes]
rs7651713	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs9819529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858544	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6771309	CD200	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111337000-111346000	Weak transcription	Thymus	Thymus
2	chr3:111337200-111344800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:111337200-111346000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:111338600-111347800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:111340400-111344800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:111341200-111346800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:111341400-111347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:111341800-111347600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:111342000-111344000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:111342000-111348000	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:111342200-111344400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:111342400-111346800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:111342600-111344400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:111342600-111345800	Strong transcription	Primary T cells from cord blood	blood
15	chr3:111342600-111347600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:111342800-111346800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:111343000-111344200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:111343000-111344200	Strong transcription	Fetal Thymus	thymus
19	chr3:111343200-111347800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:111343600-111344600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:111343600-111346000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:111343800-111346000	Strong transcription	Dnd41	blood

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