Variant report

Variant	rs2842608
Chromosome Location	chr6:86295858-86295859
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86294224..86298589-chr6:86301078..86306001,4	MCF-7	breast:
2	chr6:86294695..86297402-chr6:86376038..86378724,2	K562	blood:
3	chr6:86295157..86296902-chr6:86297407..86299649,2	K562	blood:
4	chr6:86294754..86298777-chr6:86299293..86305225,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1059306	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10944133	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10944137	0.82[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs1173415	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs11755642	0.82[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs12192546	0.82[CEU][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap]
rs12193904	0.81[CEU][hapmap]
rs12199873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12203963	0.83[CEU][hapmap]
rs12205013	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12212480	0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs12212560	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs13207173	0.82[CEU][hapmap]
rs1335442	0.82[CEU][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap]
rs1885607	0.84[EUR][1000 genomes]
rs2065114	0.91[CHB][hapmap]
rs2225754	0.82[CEU][hapmap]
rs2229523	0.90[ASN][1000 genomes]
rs2475790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2475791	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2475792	0.86[CEU][hapmap]
rs2484355	0.85[EUR][1000 genomes]
rs2758840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758842	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2758843	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2758844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758845	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2758846	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758848	0.83[CEU][hapmap]
rs2783171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842600	0.83[CEU][hapmap]
rs2842601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842602	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842603	0.86[CEU][hapmap]
rs2842604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842609	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842611	0.83[CEU][hapmap]
rs2842612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842614	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2842617	0.86[EUR][1000 genomes]
rs3087978	0.82[CEU][hapmap]
rs3812133	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4145082	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235826	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4235827	0.91[ASN][1000 genomes]
rs4304137	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4348284	0.83[CEU][hapmap]
rs4351223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs4383777	0.81[EUR][1000 genomes]
rs4419647	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4431401	0.83[CEU][hapmap]
rs4441928	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501401	0.90[ASN][1000 genomes]
rs4579322	0.89[CHB][hapmap]
rs4706240	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707207	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs4707209	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707211	0.83[CEU][hapmap]
rs4707217	0.83[EUR][1000 genomes]
rs6454469	0.84[ASN][1000 genomes]
rs6454471	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454486	0.81[EUR][1000 genomes]
rs6454487	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6909767	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6926049	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7452605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742201	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7742691	0.91[CEU][hapmap]
rs7746065	0.91[CHB][hapmap]
rs7768065	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770359	0.85[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7775864	0.86[EUR][1000 genomes]
rs911927	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9294337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9342041	0.87[EUR][1000 genomes]
rs9344532	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9344542	0.87[CEU][hapmap]
rs9351065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9353318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353320	0.85[EUR][1000 genomes]
rs9353327	0.87[CEU][hapmap]
rs9359658	0.83[EUR][1000 genomes]
rs9362230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362233	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362239	0.82[EUR][1000 genomes]
rs9444349	0.91[ASN][1000 genomes]
rs9444352	0.83[CEU][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	0.83[CEU][hapmap]
rs9450290	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs9450318	0.82[EUR][1000 genomes]
rs9450319	0.81[EUR][1000 genomes]
rs9647601	0.82[CEU][hapmap]

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	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
2	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
3	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
4	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
5	esv3351743	chr6:86286282-86308720	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2842608	SNHG5	cis	Heart Left Ventricle	GTEx
rs2842608	SNHG5	cis	Esophagus Muscularis	GTEx
rs2842608	C6orf160	cis	uninvolved skin	skin_eQTL
rs2842608	SNHG5	cis	Thyroid	GTEx
rs2842608	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2842608	SNHG5	cis	lung	GTEx
rs2842608	SNHG5	cis	Artery Tibial	GTEx
rs2842608	SNHG5	cis	Nerve Tibial	GTEx
rs2842608	SNHG5	cis	multi-tissue	Pritchard
rs2842608	C6orf160	cis	normal skin	skin_eQTL
rs2842608	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2842608	SNHG5	cis	Whole Blood	GTEx
rs2842608	C6orf160	cis	lesional skin	skin_eQTL
rs2842608	NT5E	cis	cerebellum	SCAN
rs2842608	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2842608	SNHG5	cis	Muscle Skeletal	GTEx
rs2842608	SNHG5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
3	chr6:86278200-86302600	Weak transcription	Ovary	ovary
4	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
6	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:86286800-86297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:86288200-86301400	Weak transcription	Fetal Heart	heart
9	chr6:86289200-86301000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:86289800-86297600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:86290000-86300800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:86290000-86301000	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:86290200-86301800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:86290400-86301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
16	chr6:86290800-86296400	Weak transcription	Fetal Stomach	stomach
17	chr6:86290800-86301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:86290800-86302000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:86291000-86296400	Weak transcription	Left Ventricle	heart
20	chr6:86291000-86296400	Weak transcription	Psoas Muscle	Psoas
21	chr6:86291000-86297000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:86291000-86297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:86291000-86297200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:86291000-86302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:86291000-86302000	Weak transcription	HSMM	muscle
26	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:86291200-86298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:86291200-86300600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:86291200-86301000	Weak transcription	Primary T cells from cord blood	blood
30	chr6:86291200-86301200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:86291200-86301200	Weak transcription	Hela-S3	cervix
32	chr6:86291200-86301200	Weak transcription	NHEK	skin
33	chr6:86291200-86301400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:86291200-86301800	Weak transcription	HUVEC	blood vessel
35	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
36	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:86291200-86302800	Weak transcription	Gastric	stomach
38	chr6:86291400-86300400	Weak transcription	A549	lung
39	chr6:86292000-86298600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:86292000-86299800	Weak transcription	HepG2	liver
41	chr6:86292000-86300400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:86292000-86300600	Weak transcription	K562	blood
43	chr6:86292000-86301000	Weak transcription	Primary B cells from cord blood	blood
44	chr6:86292000-86301200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:86292000-86301800	Weak transcription	NHDF-Ad	bronchial
46	chr6:86293800-86297200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:86293800-86297600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:86293800-86301000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:86294000-86297200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:86294000-86301800	Weak transcription	Brain Cingulate Gyrus	brain

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