Variant report

Variant	rs10456461
Chromosome Location	chr6:38166439-38166440
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:24)

rs_ID	r²[population]
rs10456462	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947715	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10947717	1.00[CHB][hapmap]
rs11751094	1.00[CHB][hapmap]
rs11751153	1.00[CHB][hapmap]
rs11752623	1.00[CHB][hapmap]
rs11753563	1.00[CHB][hapmap]
rs11755439	1.00[CHB][hapmap]
rs11755600	1.00[CHB][hapmap]
rs11756301	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11756626	1.00[CHB][hapmap]
rs11757654	1.00[CHB][hapmap]
rs11759816	1.00[CHB][hapmap]
rs12202202	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17757975	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1923280	1.00[CHB][hapmap]
rs1931760	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1931761	1.00[CHB][hapmap]
rs4336442	1.00[CHB][hapmap]
rs9369034	1.00[CHB][hapmap]
rs9462399	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9462403	1.00[CHB][hapmap]
rs9470765	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9470779	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10456461	MDFI	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
3	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:38141800-38168000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:38143600-38177200	Weak transcription	Ovary	ovary
6	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:38152000-38166600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:38155600-38177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:38160200-38177600	Weak transcription	Esophagus	oesophagus
10	chr6:38160400-38177000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:38160400-38177600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:38160600-38177000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:38160600-38179600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:38161200-38167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:38161600-38175200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:38162000-38179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:38162600-38167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:38162600-38167800	Weak transcription	Lung	lung
20	chr6:38162600-38180000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:38162800-38169000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:38163000-38176200	Weak transcription	Fetal Stomach	stomach
23	chr6:38164400-38166800	Strong transcription	Primary B cells from cord blood	blood
24	chr6:38165800-38166600	Weak transcription	Primary T cells from cord blood	blood

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