Variant report

Variant	rs6457816
Chromosome Location	chr6:35362848-35362849
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	chr6:35359555..35363519-chr6:35435145..35438155,4	K562	blood:
2	chr6:35360426..35363519-chr6:35436261..35438354,3	K562	blood:

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1053046	0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11571504	0.96[ASN][1000 genomes]
rs3213573	1.00[JPT][hapmap]
rs6457813	1.00[JPT][hapmap]
rs6457815	1.00[MEX][hapmap]
rs6900530	1.00[JPT][hapmap]
rs6901410	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6902123	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6906237	1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs6919334	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922548	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6937088	0.87[ASN][1000 genomes]
rs6942357	1.00[ASN][1000 genomes]
rs707969	1.00[JPT][hapmap]
rs73413718	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746988	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7754871	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296148	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296154	1.00[JPT][hapmap]
rs9470001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470007	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9658083	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9658100	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9658119	0.85[GIH][hapmap]
rs9658125	1.00[JPT][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS 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
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6457816	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35338400-35378400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:35345600-35378400	Weak transcription	Aorta	Aorta
3	chr6:35351000-35363400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:35354000-35372400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:35355000-35364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:35358000-35363400	Enhancers	HUVEC	blood vessel
7	chr6:35358400-35363000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:35359400-35363000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr6:35359400-35363000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:35359400-35363400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:35359400-35363600	Enhancers	Left Ventricle	heart
12	chr6:35359400-35363600	Enhancers	Ovary	ovary
13	chr6:35359600-35369200	Weak transcription	Fetal Kidney	kidney
14	chr6:35359800-35363000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:35359800-35363000	Genic enhancers	Placenta	Placenta
16	chr6:35359800-35363000	Enhancers	K562	blood
17	chr6:35359800-35364600	Weak transcription	NHDF-Ad	bronchial
18	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:35360000-35364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:35360000-35366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
23	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:35360200-35363200	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:35360400-35363400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:35360400-35372000	Weak transcription	Brain Angular Gyrus	brain
28	chr6:35360400-35372200	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:35360600-35365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:35360600-35372400	Weak transcription	Brain Anterior Caudate	brain
31	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:35360800-35363000	Enhancers	Fetal Thymus	thymus
33	chr6:35360800-35364600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:35360800-35367800	Weak transcription	Liver	Liver
35	chr6:35361000-35364200	Weak transcription	Fetal Intestine Small	intestine
36	chr6:35361000-35365000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:35361000-35365000	Weak transcription	Fetal Stomach	stomach
38	chr6:35361000-35365000	Weak transcription	Right Atrium	heart
39	chr6:35361000-35365400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:35361000-35378000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
42	chr6:35361000-35378600	Weak transcription	NHLF	lung
43	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
44	chr6:35361200-35363000	Weak transcription	Pancreas	Pancrea
45	chr6:35361200-35364800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:35361200-35364800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:35361200-35364800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:35361200-35376200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:35361400-35364800	Weak transcription	Fetal Muscle Leg	muscle

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