Variant report

Variant	rs2267669
Chromosome Location	chr6:35378124-35378125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35376249..35378829-chr6:35387490..35390068,2	K562	blood:
2	chr6:35376688..35379327-chr6:35465068..35467470,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1040436	0.88[CHD][hapmap]
rs1053049	0.88[CHD][hapmap]
rs1883322	0.90[CHD][hapmap]
rs2016520	0.84[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2038067	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038068	0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2076166	0.89[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076167	0.93[CHD][hapmap]
rs2076169	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267665	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267666	0.90[CHD][hapmap]
rs2267667	0.90[CHD][hapmap]
rs2267668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894401	0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap]
rs3734254	0.88[CHD][hapmap]
rs4713858	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6457819	0.86[ASN][1000 genomes]
rs6899536	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs760783	0.89[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7749160	0.89[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7749165	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751481	0.90[CHD][hapmap]
rs9380506	0.87[ASN][1000 genomes]
rs9462082	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470015	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470024	0.87[ASN][1000 genomes]
rs9794	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2267669	RNF8	cis	cerebellum	SCAN
rs2267669	C6orf106	cis	cerebellum	SCAN
rs2267669	PXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
6	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:35361000-35378600	Weak transcription	NHLF	lung
11	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
12	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
14	chr6:35362200-35378400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:35362200-35378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:35362200-35380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:35363400-35378200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:35365400-35378600	Weak transcription	NHDF-Ad	bronchial
19	chr6:35365800-35378600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:35365800-35378600	Weak transcription	Ovary	ovary
21	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:35366400-35382800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:35366600-35378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:35367800-35378600	Weak transcription	Thymus	Thymus
25	chr6:35369200-35378600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:35369200-35378800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:35369200-35379000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:35369200-35382600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:35369400-35382600	Weak transcription	NH-A	brain
30	chr6:35369600-35378200	Weak transcription	Esophagus	oesophagus
31	chr6:35370200-35378200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:35370200-35378400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:35370600-35393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:35370800-35378600	Weak transcription	Colonic Mucosa	Colon
35	chr6:35371000-35378800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:35371000-35382400	Weak transcription	Right Atrium	heart
37	chr6:35371200-35378800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:35371200-35382400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:35371200-35382400	Weak transcription	Stomach Mucosa	stomach
40	chr6:35371200-35383200	Weak transcription	Fetal Kidney	kidney
41	chr6:35371600-35378400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:35371600-35378600	Weak transcription	Left Ventricle	heart
43	chr6:35372000-35378600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:35372000-35378600	Weak transcription	Pancreas	Pancrea
45	chr6:35372000-35382400	Weak transcription	Fetal Heart	heart
46	chr6:35372400-35378200	Weak transcription	Lung	lung
47	chr6:35372800-35378200	Weak transcription	Fetal Intestine Small	intestine
48	chr6:35373200-35378200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:35373200-35381400	Weak transcription	Fetal Brain Male	brain
50	chr6:35373400-35382400	Weak transcription	Brain Germinal Matrix	brain

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