Variant report

Variant	rs2758846
Chromosome Location	chr6:86349570-86349571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:86321877..86325209-chr6:86349274..86351856,3	K562	blood:
2	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
3	chr6:86326511..86329111-chr6:86347081..86350058,3	K562	blood:
4	chr6:86300873..86305245-chr6:86347697..86356641,19	K562	blood:
5	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
6	chr6:86317763..86319413-chr6:86348369..86350869,2	K562	blood:
7	chr6:86327554..86329111-chr6:86347081..86350058,2	K562	blood:
8	chr6:86308147..86310058-chr6:86348388..86350658,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135317	Chromatin interaction
ENSG00000271793	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1059306	0.95[CEU][hapmap];0.82[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10944133	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10944137	0.84[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs1173415	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755642	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs11758508	0.83[TSI][hapmap]
rs12192546	0.84[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs12199873	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205013	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212480	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs12212560	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1335442	0.94[MKK][hapmap];0.83[TSI][hapmap]
rs1885607	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2065114	0.91[CHB][hapmap]
rs2229523	0.85[ASN][1000 genomes]
rs2475790	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2475791	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2475792	0.82[CEU][hapmap]
rs2484355	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2758840	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758842	0.86[CEU][hapmap]
rs2758843	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2758844	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758845	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2758847	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842601	0.95[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842602	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842603	0.82[CEU][hapmap]
rs2842604	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842607	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842608	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]
rs2842609	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842613	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];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842614	0.86[CEU][hapmap]
rs3812133	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145082	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235826	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4235827	0.85[ASN][1000 genomes]
rs4304137	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4351223	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs4383777	0.84[EUR][1000 genomes]
rs4419647	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4441928	0.91[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];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4501401	0.85[ASN][1000 genomes]
rs4579322	0.89[CHB][hapmap]
rs4706240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707207	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs4707209	0.83[ASN][1000 genomes]
rs4707217	0.86[EUR][1000 genomes]
rs6454471	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6454486	0.84[EUR][1000 genomes]
rs6454487	0.83[TSI][hapmap]
rs6909767	0.86[CEU][hapmap]
rs6922	0.95[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[ASN][1000 genomes]
rs6926049	0.90[ASN][1000 genomes]
rs6935918	0.86[CEU][hapmap]
rs7452605	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];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742201	0.95[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7742691	0.86[CEU][hapmap]
rs7746065	0.91[CHB][hapmap]
rs7757864	0.82[EUR][1000 genomes]
rs7768065	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7770359	0.80[ASN][1000 genomes]
rs911927	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9294337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9342046	0.81[EUR][1000 genomes]
rs9344532	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9344533	0.86[CEU][hapmap]
rs9344542	0.82[CEU][hapmap]
rs9351065	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9353318	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9353327	0.82[CEU][hapmap]
rs9362230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362233	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9362239	0.85[EUR][1000 genomes]
rs9444349	0.85[ASN][1000 genomes]
rs9450290	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450302	0.86[CEU][hapmap]
rs9450318	0.85[EUR][1000 genomes]
rs9450319	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2758846	SNHG5	cis	lung	GTEx
rs2758846	SNHG5	cis	multi-tissue	Pritchard
rs2758846	SNHG5	cis	Whole Blood	GTEx
rs2758846	NT5E	cis	cerebellum	SCAN
rs2758846	SNHG5	cis	Esophagus Muscularis	GTEx
rs2758846	SNHG5	cis	Esophagus Mucosa	GTEx
rs2758846	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2758846	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2758846	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2758846	SNHG5	cis	Heart Left Ventricle	GTEx
rs2758846	SNHG5	cis	Nerve Tibial	GTEx
rs2758846	SNHG5	cis	Muscle Skeletal	GTEx
rs2758846	C6orf160	cis	lesional skin	skin_eQTL
rs2758846	C6orf160	cis	normal skin	skin_eQTL
rs2758846	C6orf160	cis	uninvolved skin	skin_eQTL
rs2758846	SNHG5	cis	Thyroid	GTEx
rs2758846	SNHG5	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
2	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:86335200-86349600	Strong transcription	Fetal Muscle Leg	muscle
10	chr6:86340400-86350400	Weak transcription	Aorta	Aorta
11	chr6:86346200-86349800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:86346200-86350400	Weak transcription	Fetal Intestine Small	intestine
13	chr6:86346400-86350600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:86346600-86350000	Genic enhancers	HepG2	liver
15	chr6:86346600-86352400	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr6:86347000-86349800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:86347000-86349800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:86347000-86350200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:86347000-86350200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:86347000-86350200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:86347000-86350400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:86347000-86350400	Genic enhancers	Colon Smooth Muscle	Colon
23	chr6:86347000-86351200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
24	chr6:86347400-86349600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:86347400-86349600	Genic enhancers	Rectal Smooth Muscle	rectum
26	chr6:86347400-86350800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:86347600-86349800	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr6:86347800-86350200	Genic enhancers	Duodenum Mucosa	Duodenum
29	chr6:86347800-86350400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:86348200-86349600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:86348200-86349800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:86348200-86350000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:86348200-86350200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:86348200-86350400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
35	chr6:86348200-86350600	Genic enhancers	Fetal Lung	lung
36	chr6:86348200-86351600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:86348400-86349600	Genic enhancers	Brain Germinal Matrix	brain
38	chr6:86348400-86349800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
39	chr6:86348400-86350000	Genic enhancers	Primary T cells from cord blood	blood
40	chr6:86348400-86350200	Genic enhancers	NHDF-Ad	bronchial
41	chr6:86348400-86350400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr6:86348400-86351000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
43	chr6:86348400-86351600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:86348400-86351800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
45	chr6:86348600-86349600	Genic enhancers	Brain Anterior Caudate	brain
46	chr6:86348600-86349600	Strong transcription	Colonic Mucosa	Colon
47	chr6:86348600-86349600	Genic enhancers	Fetal Brain Male	brain
48	chr6:86348600-86349600	Genic enhancers	Left Ventricle	heart
49	chr6:86348600-86349600	Genic enhancers	Small Intestine	intestine
50	chr6:86348600-86349800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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