Variant report

Variant	rs3799609
Chromosome Location	chr6:166983175-166983176
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166982541..166984779-chr6:166986370..166988271,2	K562	blood:
2	chr15:91415474..91417592-chr6:166982215..166983716,2	K562	blood:

Variant related genes	Relation type
ENSG00000140564	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12661820	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799610	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166968400-166985800	Weak transcription	Fetal Kidney	kidney
2	chr6:166970800-166986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:166971000-166986000	Weak transcription	Pancreas	Pancrea
4	chr6:166972200-166986000	Weak transcription	Gastric	stomach
5	chr6:166973400-166984600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:166973800-166986000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:166974000-166989600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:166974400-166992400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:166974800-166986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:166976400-166988600	Weak transcription	Ovary	ovary
11	chr6:166977800-166985800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:166978200-166984600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:166978200-166984600	Weak transcription	Fetal Brain Female	brain
14	chr6:166978600-166983200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:166978600-166985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:166978800-166984800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:166979000-166984800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:166979000-166985800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:166979400-166996600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:166979400-166997600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:166980000-166985800	Weak transcription	Brain Substantia Nigra	brain
22	chr6:166980000-166986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:166980200-166986200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:166980400-166986000	Weak transcription	Brain Germinal Matrix	brain
25	chr6:166980600-166984800	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:166980600-166985800	Weak transcription	Brain Angular Gyrus	brain
27	chr6:166980800-166986200	Weak transcription	Right Atrium	heart
28	chr6:166981000-166985800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:166981000-166986000	Weak transcription	Brain Anterior Caudate	brain
30	chr6:166981000-166986000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:166981200-166992200	Weak transcription	HSMMtube	muscle
32	chr6:166981400-166985600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:166981400-166985600	Weak transcription	Osteobl	bone
34	chr6:166981400-166985800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:166981400-166986000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:166981400-166986000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:166981600-166983600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:166981600-166984600	Weak transcription	HUVEC	blood vessel
39	chr6:166981600-166984600	Weak transcription	NH-A	brain
40	chr6:166981600-166985400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:166981600-166985800	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:166981600-166985800	Weak transcription	Fetal Stomach	stomach
43	chr6:166981600-166985800	Weak transcription	NHDF-Ad	bronchial
44	chr6:166981600-166986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:166981600-166986000	Weak transcription	Right Ventricle	heart
46	chr6:166981600-166986000	Weak transcription	HSMM	muscle
47	chr6:166981800-166983200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:166981800-166984400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:166981800-166984600	Weak transcription	HMEC	breast
50	chr6:166981800-166985600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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