Variant report

Variant	rs4296866
Chromosome Location	chr6:86279737-86279738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86278825..86281337-chr6:86301829..86304998,5	MCF-7	breast:
2	chr6:86272075..86276621-chr6:86278796..86281589,4	K562	blood:
3	chr6:86277967..86280027-chr6:86387160..86389820,3	K562	blood:
4	chr6:86278096..86280709-chr6:86299065..86302030,2	K562	blood:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1059307	0.87[GIH][hapmap]
rs10944128	0.83[GIH][hapmap]
rs11752795	0.81[AFR][1000 genomes]
rs2758848	0.85[GIH][hapmap]
rs2842600	0.85[GIH][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs2842611	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]
rs4348284	0.82[YRI][hapmap]
rs4431401	0.81[GIH][hapmap]
rs6454472	0.83[GIH][hapmap]
rs7766485	0.83[GIH][hapmap]
rs9444352	0.85[GIH][hapmap]
rs9450285	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs4296866	SNHG5	cis	Nerve Tibial	GTEx
rs4296866	KIAA1009	cis	cerebellum	SCAN
rs4296866	SNORD50B	cis	parietal	SCAN
rs4296866	C6orf160	cis	lesional skin	skin_eQTL
rs4296866	SNHG5	cis	Whole Blood	GTEx
rs4296866	SNHG5	cis	Artery Tibial	GTEx
rs4296866	SNORD50A	cis	cerebellum	SCAN
rs4296866	SNHG5	cis	Thyroid	GTEx
rs4296866	SNHG5	cis	multi-tissue	Pritchard
rs4296866	C6orf160	cis	uninvolved skin	skin_eQTL
rs4296866	C6orf160	cis	multi-tissue	Pritchard
rs4296866	SNHG5	cis	Esophagus Muscularis	GTEx
rs4296866	SNHG5	cis	Muscle Skeletal	GTEx
rs4296866	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4296866	SNHG5	cis	lymphoblastoid	seeQTL
rs4296866	SNHG5	cis	Adipose Subcutaneous	GTEx
rs4296866	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4296866	SNHG5	cis	lung	GTEx
rs4296866	SNHG5	cis	Heart Left Ventricle	GTEx
rs4296866	C6orf160	cis	normal skin	skin_eQTL
rs4296866	SNHG5	cis	Esophagus Mucosa	GTEx
rs4296866	SNHG5	cis	Artery Aorta	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
2	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
3	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
4	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:86223400-86285000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
7	chr6:86231200-86285000	Weak transcription	Hela-S3	cervix
8	chr6:86233800-86289200	Weak transcription	Spleen	Spleen
9	chr6:86241400-86283600	Weak transcription	Fetal Kidney	kidney
10	chr6:86243200-86285200	Weak transcription	Psoas Muscle	Psoas
11	chr6:86243200-86286000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
13	chr6:86243600-86285000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:86243600-86285800	Weak transcription	Fetal Brain Female	brain
15	chr6:86243600-86286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:86243800-86284800	Weak transcription	Brain Angular Gyrus	brain
17	chr6:86244200-86286000	Weak transcription	Right Ventricle	heart
18	chr6:86244200-86289200	Weak transcription	Gastric	stomach
19	chr6:86244400-86281000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:86250200-86284800	Weak transcription	Aorta	Aorta
21	chr6:86252800-86284400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:86252800-86289600	Weak transcription	Esophagus	oesophagus
23	chr6:86253400-86286000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:86254800-86287800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:86257600-86285200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:86258000-86280600	Weak transcription	HepG2	liver
27	chr6:86258000-86284800	Weak transcription	Fetal Heart	heart
28	chr6:86258000-86286000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:86258400-86284400	Weak transcription	A549	lung
30	chr6:86258600-86283200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:86260600-86281600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:86263000-86281000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:86263000-86284600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:86263000-86284800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:86263000-86289400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:86263000-86289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:86263200-86280800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:86263200-86282200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:86265600-86288200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:86265600-86289800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:86266000-86281200	Weak transcription	K562	blood
42	chr6:86266400-86290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:86269200-86283400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:86269600-86281800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:86270400-86286200	Weak transcription	Brain Anterior Caudate	brain
46	chr6:86271800-86280400	Weak transcription	Placenta	Placenta
47	chr6:86272000-86284800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:86272000-86290200	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:86272200-86286200	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:86272600-86280600	Weak transcription	Fetal Stomach	stomach

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