Variant report

Variant	rs3817780
Chromosome Location	chr6:166905456-166905457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10946174	0.84[GIH][hapmap]
rs2072830	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072832	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072833	0.84[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2235275	0.82[CHB][hapmap]
rs2235276	0.95[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2235277	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2281045	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35665106	0.88[EUR][1000 genomes]
rs3765235	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3799671	0.93[EUR][1000 genomes]
rs3817778	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3817781	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817783	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817786	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4710056	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9347130	0.88[EUR][1000 genomes]

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	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	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886939	chr6:166859725-166922813	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166862400-166920600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:166877200-166908800	Weak transcription	Colonic Mucosa	Colon
4	chr6:166884600-166911400	Weak transcription	HMEC	breast
5	chr6:166890600-166925200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:166892600-166910600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:166893000-166923200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:166893600-166921400	Weak transcription	Fetal Brain Male	brain
9	chr6:166894800-166928400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:166896400-166906000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:166897000-166908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:166897600-166922400	Weak transcription	HSMMtube	muscle
13	chr6:166899400-166929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:166899600-166907200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:166899600-166907200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:166900400-166907800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:166900600-166912200	Weak transcription	Fetal Intestine Large	intestine
18	chr6:166901000-166906600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:166901000-166906600	Weak transcription	Fetal Intestine Small	intestine
20	chr6:166901000-166907000	Weak transcription	Liver	Liver
21	chr6:166901000-166907200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:166901000-166907800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:166901000-166911800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:166901400-166922000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:166901600-166906000	Enhancers	HUVEC	blood vessel
27	chr6:166901600-166907200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:166901800-166905800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:166902400-166906400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:166902400-166917600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:166902400-166922600	Weak transcription	Thymus	Thymus
33	chr6:166902400-166923600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:166902600-166907000	Weak transcription	NHLF	lung
35	chr6:166902600-166908400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:166902600-166910800	Weak transcription	Primary T cells from cord blood	blood
37	chr6:166902600-166910800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:166902600-166916800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:166902800-166909200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:166903000-166915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:166903000-166919200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:166903000-166925400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:166903200-166916000	Weak transcription	NHDF-Ad	bronchial
45	chr6:166903400-166906000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:166903400-166907600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:166903600-166907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:166903600-166916200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:166903800-166905600	Strong transcription	Fetal Brain Female	brain
50	chr6:166903800-166908800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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