Variant report

Variant	rs10947749
Chromosome Location	chr6:38505805-38505806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10484856	0.92[CEU][hapmap]
rs1073900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154188	0.88[CEU][hapmap]
rs12193868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12206218	0.92[CEU][hapmap]
rs12206371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208087	0.92[CEU][hapmap]
rs1406841	0.92[CEU][hapmap]
rs1590165	0.85[YRI][hapmap]
rs17543429	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2748156	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2748161	0.83[EUR][1000 genomes]
rs2748173	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2814882	0.83[EUR][1000 genomes]
rs2814887	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814890	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4074421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4236061	0.81[EUR][1000 genomes]
rs4254983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869483	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083119	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56250767	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458060	0.80[CEU][hapmap]
rs6903004	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs6924443	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6927145	0.86[CEU][hapmap]
rs72853429	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752239	0.88[CEU][hapmap];0.85[YRI][hapmap]
rs7755619	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs7761154	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7767041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769475	0.85[YRI][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38479000-38509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:38487000-38518600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38492800-38508000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:38494400-38513800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:38494400-38515400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:38494400-38518800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:38494400-38524200	Weak transcription	Aorta	Aorta
8	chr6:38494800-38522600	Weak transcription	Ovary	ovary
9	chr6:38495000-38521800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:38496200-38517600	Weak transcription	Esophagus	oesophagus
11	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:38496800-38521600	Weak transcription	Lung	lung
13	chr6:38497000-38517600	Weak transcription	Small Intestine	intestine
14	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38498400-38518400	Weak transcription	Primary B cells from cord blood	blood
17	chr6:38500600-38506600	Weak transcription	Gastric	stomach
18	chr6:38500600-38514800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:38500600-38517600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:38500600-38517600	Weak transcription	Right Ventricle	heart
21	chr6:38500600-38518600	Weak transcription	Left Ventricle	heart
22	chr6:38500800-38520800	Weak transcription	Fetal Intestine Small	intestine
23	chr6:38501400-38518600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:38505800-38506200	Enhancers	Brain Germinal Matrix	brain

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