Variant report

Variant	rs9858544
Chromosome Location	chr3:111330922-111330923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11914473	0.97[ASN][1000 genomes]
rs1513328	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858327	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs16858329	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16858353	0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2895386	0.96[ASN][1000 genomes]
rs3733176	0.88[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56172864	0.97[ASN][1000 genomes]
rs56306480	0.97[ASN][1000 genomes]
rs57067927	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57501419	0.99[ASN][1000 genomes]
rs57831621	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763322	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6765832	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6768092	0.97[ASN][1000 genomes]
rs6770144	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6770679	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771309	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]
rs6780210	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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780729	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787870	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6801876	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73230132	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73230143	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73852844	0.97[ASN][1000 genomes]
rs73852849	0.97[ASN][1000 genomes]
rs7431849	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637536	0.85[ASN][1000 genomes]
rs9819529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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
rs9858544	CD200	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111324400-111336800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:111329600-111331000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111329800-111331000	Genic enhancers	Primary T cells from cord blood	blood
4	chr3:111329800-111331000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:111329800-111331000	Genic enhancers	Fetal Thymus	thymus
6	chr3:111329800-111331200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:111329800-111333600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:111330000-111331000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:111330000-111334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:111330200-111331000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr3:111330200-111331000	Genic enhancers	Thymus	Thymus
12	chr3:111330200-111331000	Enhancers	NHEK	skin
13	chr3:111330200-111331400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:111330200-111334400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:111330200-111334600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:111330400-111332400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:111330400-111334400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:111330600-111332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:111330600-111333600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:111330600-111333800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:111330600-111334200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:111330600-111335000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:111330800-111331600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:111330800-111333000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:111330800-111333400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:111330800-111333600	Strong transcription	Dnd41	blood
27	chr3:111330800-111335200	Weak transcription	HMEC	breast

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