Variant report

Variant	rs2842611
Chromosome Location	chr6:86302034-86302035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:86301666-86302301	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:86301749-86302154	HepG2	liver:	n/a	chr6:86301823-86301835
3	FOXA2	chr6:86301741-86302110	HepG2	liver:	n/a	chr6:86301823-86301835
4	MAFK	chr6:86301946-86302272	K562	blood:	n/a	n/a
5	FOXA1	chr6:86301643-86302129	HepG2	liver:	n/a	chr6:86301823-86301835
6	POLR2A	chr6:86301932-86302067	HepG2	liver:	n/a	n/a
7	MXI1	chr6:86301986-86304867	SK-N-SH	brain:	n/a	n/a
8	FOXA1	chr6:86301698-86302168	HepG2	liver:	n/a	chr6:86301823-86301835

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86252970..86257934-chr6:86299533..86304034,5	K562	blood:
2	chr6:86299824..86305374-chr6:86350530..86356322,11	MCF-7	breast:
3	chr16:89630470..89633084-chr6:86301680..86303446,2	MCF-7	breast:
4	chr6:86301331..86304881-chr6:86350851..86355985,12	MCF-7	breast:
5	chr6:86300286..86310605-chr6:86384413..86390498,39	K562	blood:
6	chr6:86299850..86302872-chr6:86358961..86362964,3	K562	blood:
7	chr6:86191399..86193392-chr6:86300815..86302853,2	K562	blood:
8	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
9	chr6:86301325..86305014-chr6:86385299..86388840,4	MCF-7	breast:
10	chr6:86300873..86305245-chr6:86347697..86356641,19	K562	blood:
11	chr6:86284643..86286706-chr6:86299863..86303229,3	K562	blood:
12	chr6:86298349..86307534-chr6:86383938..86391964,31	K562	blood:
13	chr6:86298806..86300763-chr6:86301374..86304077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNX14	TF binding region
ENSG00000203875	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1059306	0.83[CEU][hapmap]
rs1059307	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10944128	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10944129	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs1173418	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs11752795	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12193777	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12199873	0.83[CEU][hapmap]
rs12203963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12206573	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12212560	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2475790	0.83[CEU][hapmap]
rs2475792	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs2758840	0.83[CEU][hapmap]
rs2758842	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs2758843	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2758845	0.91[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2758847	0.83[CEU][hapmap]
rs2758848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2758849	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783171	0.83[CEU][hapmap]
rs2842600	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842601	0.83[CEU][hapmap]
rs2842603	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2842605	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842607	0.83[CEU][hapmap]
rs2842608	0.83[CEU][hapmap]
rs2842609	0.83[CEU][hapmap]
rs2842610	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842612	0.82[CEU][hapmap]
rs2842613	0.83[CEU][hapmap]
rs2842614	0.91[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs2842615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3087978	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34980280	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4296866	0.83[ASW][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4304137	0.83[CEU][hapmap]
rs4348284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4351223	0.83[CEU][hapmap]
rs4431401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4593336	0.84[CHD][hapmap]
rs4640862	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707212	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454471	0.83[CEU][hapmap]
rs6454472	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909767	0.91[CEU][hapmap]
rs6922	0.83[CEU][hapmap]
rs6927475	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs7452605	0.83[CEU][hapmap]
rs7742201	0.82[CEU][hapmap]
rs7742691	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs7766485	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs7775864	0.87[CHB][hapmap]
rs911927	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9294337	0.83[CEU][hapmap]
rs9342045	0.88[EUR][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs9344540	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9344542	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs9351065	0.83[CEU][hapmap]
rs9353318	0.83[CEU][hapmap]
rs9353327	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs9362230	0.83[CEU][hapmap]
rs9362232	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444348	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9444351	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444354	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450273	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs9450282	0.84[CHD][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450288	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450292	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9450311	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

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
rs2842611	SNHG5	cis	Muscle Skeletal	GTEx
rs2842611	SNHG5	cis	Artery Tibial	GTEx
rs2842611	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2842611	SNHG5	cis	multi-tissue	Pritchard
rs2842611	SNORD50B	cis	parietal	SCAN
rs2842611	SNHG5	cis	Esophagus Mucosa	GTEx
rs2842611	SNHG5	cis	Thyroid	GTEx
rs2842611	SNHG5	cis	Artery Aorta	GTEx
rs2842611	SNHG5	cis	Heart Left Ventricle	GTEx
rs2842611	SNHG5	cis	lymphoblastoid	seeQTL
rs2842611	SNHG5	cis	Whole Blood	GTEx
rs2842611	SNHG5	cis	Stomach	GTEx
rs2842611	SNHG5	cis	Esophagus Muscularis	GTEx
rs2842611	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2842611	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2842611	SNHG5	cis	lung	GTEx
rs2842611	SNHG5	cis	Nerve Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86278200-86302600	Weak transcription	Ovary	ovary
3	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
4	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
6	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:86291200-86302800	Weak transcription	Gastric	stomach
8	chr6:86297800-86302200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:86297800-86302600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:86298600-86302400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:86298800-86302600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:86299400-86302600	Weak transcription	Spleen	Spleen
13	chr6:86300400-86302200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:86300400-86302600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:86300600-86302600	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:86300600-86302600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:86300600-86302600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:86300600-86302600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:86300800-86302200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr6:86300800-86302200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:86301000-86302200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:86301000-86302600	Enhancers	Primary B cells from cord blood	blood
23	chr6:86301000-86302600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:86301000-86302600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:86301200-86302200	Enhancers	Brain Anterior Caudate	brain
26	chr6:86301200-86302400	Enhancers	Fetal Lung	lung
27	chr6:86301200-86302600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:86301200-86302600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:86301200-86302600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:86301200-86302600	Enhancers	Adipose Nuclei	Adipose
31	chr6:86301200-86302600	Enhancers	Brain Substantia Nigra	brain
32	chr6:86301400-86302200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:86301400-86302200	Enhancers	Fetal Heart	heart
34	chr6:86301400-86302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:86301400-86302400	Enhancers	Thymus	Thymus
36	chr6:86301400-86302600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr6:86301400-86302600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:86301600-86302200	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr6:86301600-86302400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:86301600-86302400	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:86301600-86302400	Enhancers	Fetal Thymus	thymus
42	chr6:86301600-86302600	Weak transcription	Aorta	Aorta
43	chr6:86301600-86302600	Enhancers	Small Intestine	intestine
44	chr6:86301600-86303600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:86301800-86302200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr6:86301800-86302200	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:86301800-86302200	Flanking Active TSS	Fetal Brain Female	brain
48	chr6:86301800-86302200	Enhancers	Fetal Intestine Small	intestine
49	chr6:86301800-86302200	Flanking Active TSS	Fetal Kidney	kidney
50	chr6:86301800-86302200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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