Variant report

Variant	rs6909767
Chromosome Location	chr6:86228109-86228110
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	chr6:86226272..86228604-chr6:86231901..86233578,2	K562	blood:
2	chr6:86227398..86231196-chr6:86231483..86235507,4	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1059306	0.91[CEU][hapmap]
rs1059307	0.87[CEU][hapmap]
rs10944128	0.83[CEU][hapmap]
rs1173417	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1173418	0.83[CEU][hapmap]
rs12199873	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12203963	0.91[CEU][hapmap]
rs12205013	0.82[EUR][1000 genomes]
rs12212560	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2475790	0.91[CEU][hapmap]
rs2475792	0.95[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2758840	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2758842	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2758844	0.82[EUR][1000 genomes]
rs2758845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758846	0.86[CEU][hapmap]
rs2758847	0.91[CEU][hapmap]
rs2758848	0.91[CEU][hapmap]
rs2783171	0.91[CEU][hapmap]
rs2842600	0.91[CEU][hapmap]
rs2842601	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2842602	0.82[EUR][1000 genomes]
rs2842603	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842604	0.86[CEU][hapmap]
rs2842607	0.91[CEU][hapmap]
rs2842608	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2842609	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2842611	0.91[CEU][hapmap]
rs2842612	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2842613	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842614	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842617	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3087978	0.91[CEU][hapmap]
rs3812133	0.86[CEU][hapmap]
rs4304137	0.91[CEU][hapmap]
rs4348284	0.91[CEU][hapmap]
rs4351223	0.91[CEU][hapmap]
rs4373337	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4419647	0.87[EUR][1000 genomes]
rs4431401	0.91[CEU][hapmap]
rs4441928	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4593336	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs4706240	0.80[EUR][1000 genomes]
rs4707211	0.91[CEU][hapmap]
rs6454467	0.81[ASN][1000 genomes]
rs6454471	0.91[CEU][hapmap]
rs6454472	0.87[CEU][hapmap]
rs6454473	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6922	0.91[CEU][hapmap]
rs6935918	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7452605	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7742691	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752502	0.86[EUR][1000 genomes]
rs7757864	0.89[EUR][1000 genomes]
rs7762321	0.85[EUR][1000 genomes]
rs7766485	0.87[CEU][hapmap]
rs7768065	0.84[EUR][1000 genomes]
rs7771612	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775864	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs911927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294337	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9342041	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344532	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs9344533	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9344542	0.95[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9351065	0.91[CEU][hapmap]
rs9353318	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9353320	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9353327	0.95[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9359658	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9362230	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs9444352	0.91[CEU][hapmap]
rs9450282	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9450285	0.91[CEU][hapmap]
rs9450287	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9450290	0.86[EUR][1000 genomes]
rs9450302	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
15	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6909767	SNHG5	cis	Adipose Subcutaneous	GTEx
rs6909767	SNHG5	cis	Whole Blood	GTEx
rs6909767	SNHG5	cis	Heart Left Ventricle	GTEx
rs6909767	C6orf160	cis	lesional skin	skin_eQTL
rs6909767	SNHG5	cis	Artery Aorta	GTEx
rs6909767	SNHG5	cis	Esophagus Mucosa	GTEx
rs6909767	SNHG5	cis	Nerve Tibial	GTEx
rs6909767	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs6909767	SNHG5	cis	Esophagus Muscularis	GTEx
rs6909767	SNHG5	cis	lung	GTEx
rs6909767	SNHG5	cis	Muscle Skeletal	GTEx
rs6909767	C6orf160	cis	uninvolved skin	skin_eQTL
rs6909767	C6orf160	cis	normal skin	skin_eQTL
rs6909767	SNHG5	cis	Artery Tibial	GTEx
rs6909767	SNHG5	cis	Thyroid	GTEx
rs6909767	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs6909767	SNHG5	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
3	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
4	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
5	chr6:86211400-86246400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:86212000-86228600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:86212000-86246600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:86218000-86260200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:86219200-86246200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:86220200-86252400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:86220200-86257200	Weak transcription	Fetal Heart	heart
13	chr6:86221000-86245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:86221400-86242800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
16	chr6:86222200-86232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:86222200-86232400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:86222200-86249800	Weak transcription	Aorta	Aorta
19	chr6:86222400-86229200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:86222600-86229200	Weak transcription	Fetal Intestine Small	intestine
21	chr6:86222600-86233200	Weak transcription	Fetal Stomach	stomach
22	chr6:86222600-86243800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:86222800-86229600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:86223000-86242600	Weak transcription	Right Ventricle	heart
26	chr6:86223200-86231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:86223200-86231000	Weak transcription	Ovary	ovary
28	chr6:86223200-86233200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:86223200-86235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:86223200-86242200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:86223200-86242200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:86223200-86242600	Weak transcription	Psoas Muscle	Psoas
33	chr6:86223200-86242600	Weak transcription	Thymus	Thymus
34	chr6:86223200-86243000	Weak transcription	Brain Angular Gyrus	brain
35	chr6:86223200-86260200	Weak transcription	Lung	lung
36	chr6:86223400-86229000	Weak transcription	Fetal Intestine Large	intestine
37	chr6:86223400-86230200	Weak transcription	HSMMtube	muscle
38	chr6:86223400-86230400	Weak transcription	Fetal Lung	lung
39	chr6:86223400-86230800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:86223400-86231000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:86223400-86231600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:86223400-86231600	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:86223400-86232000	Weak transcription	Fetal Kidney	kidney
44	chr6:86223400-86232400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:86223400-86232600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:86223400-86233200	Weak transcription	Fetal Brain Female	brain
47	chr6:86223400-86233200	Weak transcription	Spleen	Spleen
48	chr6:86223400-86262800	Weak transcription	Stomach Mucosa	stomach
49	chr6:86223400-86285000	Weak transcription	Brain Substantia Nigra	brain
50	chr6:86223600-86231600	Weak transcription	NH-A	brain

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