Variant report

Variant	rs2267665
Chromosome Location	chr6:35369491-35369492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35364935..35367587-chr6:35369436..35372009,4	K562	blood:
2	chr6:35368369..35371007-chr6:35374165..35376691,3	K562	blood:
3	chr6:35369022..35371530-chr6:35380488..35382015,2	MCF-7	breast:
4	chr6:35307588..35310210-chr6:35369138..35372365,3	K562	blood:
5	chr6:35369456..35371995-chr6:35391240..35394220,2	MCF-7	breast:
6	chr6:35327509..35329101-chr6:35368128..35370568,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1040436	0.88[CHD][hapmap]
rs1053049	0.83[CHD][hapmap]
rs1883322	0.91[CHD][hapmap]
rs2016520	0.84[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2038067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038068	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs2076166	0.94[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2076167	0.88[CHD][hapmap]
rs2076169	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267666	0.91[CHD][hapmap]
rs2267667	0.91[CHD][hapmap]
rs2267668	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];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267669	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]
rs2894401	0.81[CHD][hapmap];0.83[LWK][hapmap]
rs3734254	0.83[CHD][hapmap]
rs4713858	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs6899536	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs760783	0.88[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7749160	0.94[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7749165	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7751481	0.91[CHD][hapmap]
rs9380506	0.93[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs9462082	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470024	0.81[ASN][1000 genomes]
rs9794	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2267665	PXT1	cis	lymphoblastoid	seeQTL
rs2267665	C6orf106	cis	cerebellum	SCAN

Chromatin state (count:88 , 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	chr6:35354000-35372400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
7	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:35360400-35372000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:35360400-35372200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:35360600-35372400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:35361000-35378000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
15	chr6:35361000-35378600	Weak transcription	NHLF	lung
16	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
17	chr6:35361200-35376200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
20	chr6:35362000-35378000	Weak transcription	Spleen	Spleen
21	chr6:35362200-35378400	Weak transcription	Primary B cells from cord blood	blood
22	chr6:35362200-35378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:35362200-35380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:35362800-35370200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:35363400-35378200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:35363800-35371600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:35364000-35378000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:35365400-35375800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:35365400-35378600	Weak transcription	NHDF-Ad	bronchial
30	chr6:35365600-35370200	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:35365800-35370600	Weak transcription	Gastric	stomach
32	chr6:35365800-35377800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:35365800-35378600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:35365800-35378600	Weak transcription	Ovary	ovary
35	chr6:35366000-35370000	Weak transcription	Colonic Mucosa	Colon
36	chr6:35366000-35370600	Weak transcription	Right Atrium	heart
37	chr6:35366200-35378000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:35366400-35382800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:35366600-35376600	Weak transcription	K562	blood
41	chr6:35366600-35378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:35367800-35370200	Enhancers	Liver	Liver
43	chr6:35367800-35370600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:35367800-35371000	Enhancers	HMEC	breast
45	chr6:35367800-35371600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:35367800-35372800	Strong transcription	Primary T cells from cord blood	blood
47	chr6:35367800-35378600	Weak transcription	Thymus	Thymus
48	chr6:35368000-35370400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:35368000-35371000	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:35368000-35372000	Enhancers	Fetal Heart	heart

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