Variant report

Variant	rs4348284
Chromosome Location	chr6:86350394-86350395
allele	C/T
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	chr6:86300873..86305245-chr6:86347697..86356641,19	K562	blood:
4	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
5	chr6:86317763..86319413-chr6:86348369..86350869,2	K562	blood:
6	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:
7	chr6:86322096..86325209-chr6:86349720..86353694,5	K562	blood:
8	chr6:86308147..86310058-chr6:86348388..86350658,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000271793	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000220563	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1059306	0.84[CEU][hapmap]
rs1059307	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10944128	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10944129	0.82[EUR][1000 genomes]
rs1173416	0.81[EUR][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs1173418	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs11752795	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193777	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12199873	0.84[CEU][hapmap]
rs12203963	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12206573	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212560	0.96[CEU][hapmap]
rs2475790	0.84[CEU][hapmap]
rs2475792	0.86[CEU][hapmap]
rs2758840	0.83[CEU][hapmap]
rs2758842	0.91[CEU][hapmap]
rs2758843	0.92[CEU][hapmap]
rs2758845	0.91[CEU][hapmap]
rs2758847	0.83[CEU][hapmap]
rs2758848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758849	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783171	0.83[CEU][hapmap]
rs2842600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842601	0.83[CEU][hapmap]
rs2842603	0.88[CEU][hapmap]
rs2842605	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2842607	0.83[CEU][hapmap]
rs2842608	0.83[CEU][hapmap]
rs2842609	0.84[CEU][hapmap]
rs2842610	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842611	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]
rs2842612	0.82[CEU][hapmap]
rs2842613	0.83[CEU][hapmap]
rs2842614	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs2842615	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087978	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34980280	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296866	0.82[YRI][hapmap]
rs4304137	0.84[CEU][hapmap]
rs4351223	0.83[CEU][hapmap]
rs4431401	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4640862	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707211	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707212	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454471	0.84[CEU][hapmap]
rs6454472	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6909767	0.91[CEU][hapmap]
rs6922	0.83[CEU][hapmap]
rs6927475	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap]
rs7452605	0.83[CEU][hapmap]
rs7742201	0.82[CEU][hapmap]
rs7742691	0.95[CEU][hapmap]
rs7766485	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap]
rs7775864	0.82[CHB][hapmap]
rs911927	0.92[CEU][hapmap]
rs9294337	0.84[CEU][hapmap]
rs9342045	0.92[EUR][1000 genomes]
rs9344533	0.91[CEU][hapmap]
rs9344540	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9344542	0.87[CEU][hapmap]
rs9351065	0.83[CEU][hapmap]
rs9353327	0.87[CEU][hapmap]
rs9362230	0.83[CEU][hapmap]
rs9362232	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444348	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9444351	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444354	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450284	0.83[CEU][hapmap]
rs9450285	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450288	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9450292	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450302	0.92[CEU][hapmap]
rs9450311	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4348284	SNHG5	cis	lung	GTEx
rs4348284	SNHG5	cis	Esophagus Muscularis	GTEx
rs4348284	SNHG5	cis	Whole Blood	GTEx
rs4348284	SNHG5	cis	Adipose Subcutaneous	GTEx
rs4348284	SNHG5	cis	Artery Tibial	GTEx
rs4348284	SNHG5	cis	Artery Aorta	GTEx
rs4348284	SNHG5	cis	Nerve Tibial	GTEx
rs4348284	SNHG5	cis	Heart Left Ventricle	GTEx
rs4348284	SNHG5	cis	Muscle Skeletal	GTEx
rs4348284	SNHG5	cis	Stomach	GTEx
rs4348284	SNHG5	cis	Esophagus Mucosa	GTEx
rs4348284	SNHG5	cis	Thyroid	GTEx
rs4348284	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4348284	C6orf160	cis	lesional skin	skin_eQTL
rs4348284	C6orf160	cis	uninvolved skin	skin_eQTL
rs4348284	C6orf160	cis	normal skin	skin_eQTL
rs4348284	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4348284	SNHG5	cis	multi-tissue	Pritchard

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	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:86340400-86350400	Weak transcription	Aorta	Aorta
5	chr6:86346200-86350400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:86346400-86350600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:86346600-86352400	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr6:86347000-86350400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:86347000-86350400	Genic enhancers	Colon Smooth Muscle	Colon
10	chr6:86347000-86351200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr6:86347400-86350800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:86347800-86350400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:86348200-86350400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
14	chr6:86348200-86350600	Genic enhancers	Fetal Lung	lung
15	chr6:86348200-86351600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:86348400-86350400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:86348400-86351000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
18	chr6:86348400-86351600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:86348400-86351800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
20	chr6:86348600-86350400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:86348600-86350600	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:86348600-86350600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:86348600-86350600	Genic enhancers	Liver	Liver
24	chr6:86348600-86350800	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:86348800-86350400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:86348800-86350400	Weak transcription	Right Atrium	heart
27	chr6:86348800-86351000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
28	chr6:86349000-86350400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:86349000-86350400	Weak transcription	Psoas Muscle	Psoas
30	chr6:86349000-86350400	Genic enhancers	HSMM	muscle
31	chr6:86349000-86350400	Genic enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:86349000-86350600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:86349000-86350800	Strong transcription	Placenta	Placenta
34	chr6:86349000-86350800	Transcr. at gene 5' and 3'	HMEC	breast
35	chr6:86349000-86351000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
36	chr6:86349000-86351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:86349000-86351200	Weak transcription	Gastric	stomach
38	chr6:86349000-86351200	Weak transcription	Lung	lung
39	chr6:86349000-86351200	Weak transcription	Pancreas	Pancrea
40	chr6:86349000-86351600	Transcr. at gene 5' and 3'	K562	blood
41	chr6:86349000-86354600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:86349200-86350400	Genic enhancers	Primary hematopoietic stem cells	blood
43	chr6:86349200-86350400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
44	chr6:86349200-86350400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr6:86349200-86350400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:86349200-86350800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:86349200-86351000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:86349200-86351200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
49	chr6:86349200-86351600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
50	chr6:86349200-86353000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell

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