Variant report

Variant	rs9450302
Chromosome Location	chr6:86289673-86289674
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86286722..86289673-chr6:86387180..86389276,2	MCF-7	breast:
2	chr6:86287818..86291892-chr6:86385672..86390313,6	MCF-7	breast:
3	chr6:86281475..86283897-chr6:86288113..86290341,2	K562	blood:
4	chr6:86288405..86291520-chr6:86301409..86305260,4	K562	blood:
5	chr6:86286697..86290056-chr6:86301886..86305465,5	MCF-7	breast:
6	chr6:86289336..86292710-chr6:86302948..86306481,4	MCF-7	breast:
7	chr6:86287653..86290758-chr6:86386971..86389926,3	K562	blood:
8	chr6:86288404..86291892-chr6:86352318..86354794,4	MCF-7	breast:
9	chr6:86285488..86287926-chr6:86288888..86290773,2	MCF-7	breast:
10	chr6:86279748..86283159-chr6:86286791..86290808,4	K562	blood:
11	chr6:86288385..86291520-chr6:86301409..86305260,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135317	Chromatin interaction
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1059306	0.91[CEU][hapmap]
rs1059307	0.87[CEU][hapmap]
rs10944128	0.83[CEU][hapmap]
rs1173417	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs1173418	0.84[CEU][hapmap]
rs12199873	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs12203963	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs12205013	0.84[EUR][1000 genomes]
rs12212560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13198956	1.00[YRI][hapmap]
rs16876340	1.00[YRI][hapmap]
rs16876385	1.00[YRI][hapmap]
rs1793	0.89[YRI][hapmap]
rs2475790	0.91[CEU][hapmap]
rs2475792	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2758840	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2758842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2758844	0.84[EUR][1000 genomes]
rs2758845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758846	0.86[CEU][hapmap]
rs2758847	0.91[CEU][hapmap]
rs2758848	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2783171	0.91[CEU][hapmap]
rs2842600	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2842601	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2842602	0.84[EUR][1000 genomes]
rs2842603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842604	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2842607	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2842608	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842609	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842611	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2842612	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2842613	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2842614	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2842617	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3087978	0.91[CEU][hapmap]
rs3812133	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs3900740	1.00[YRI][hapmap]
rs4304137	0.91[CEU][hapmap]
rs4348284	0.92[CEU][hapmap]
rs4351223	0.91[CEU][hapmap]
rs4373337	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4419647	0.83[EUR][1000 genomes]
rs4431401	0.91[CEU][hapmap]
rs4441928	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4593336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4706240	0.84[EUR][1000 genomes]
rs4707211	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs4707213	1.00[YRI][hapmap]
rs6454471	0.91[CEU][hapmap]
rs6454472	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs6454473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6909767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6922	0.91[CEU][hapmap]
rs6935918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7452605	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7740830	1.00[YRI][hapmap]
rs7742201	0.91[CEU][hapmap]
rs7742691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752502	0.88[EUR][1000 genomes]
rs7757864	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7762321	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7766485	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs7768065	0.86[EUR][1000 genomes]
rs7771577	1.00[YRI][hapmap]
rs7771612	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7775864	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs911927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9294337	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9342041	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9344532	0.86[CEU][hapmap]
rs9344533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344542	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9351065	0.91[CEU][hapmap]
rs9353318	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9353320	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353327	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9359658	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9362230	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9444352	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9450282	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9450285	0.91[CEU][hapmap]
rs9450287	0.89[ASN][1000 genomes]
rs9450288	0.83[CHB][hapmap]
rs9450290	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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
rs9450302	SNHG5	cis	Nerve Tibial	GTEx
rs9450302	SNHG5	cis	Adipose Subcutaneous	GTEx
rs9450302	SNHG5	cis	Heart Left Ventricle	GTEx
rs9450302	C6orf160	cis	uninvolved skin	skin_eQTL
rs9450302	SNHG5	cis	Esophagus Mucosa	GTEx
rs9450302	SNHG5	cis	lung	GTEx
rs9450302	SNHG5	cis	Artery Tibial	GTEx
rs9450302	SNHG5	cis	multi-tissue	Pritchard
rs9450302	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs9450302	C6orf160	cis	normal skin	skin_eQTL
rs9450302	SNHG5	cis	Whole Blood	GTEx
rs9450302	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs9450302	SNHG5	cis	Thyroid	GTEx
rs9450302	SNHG5	cis	Artery Aorta	GTEx
rs9450302	SNHG5	cis	Esophagus Muscularis	GTEx
rs9450302	C6orf160	cis	lesional skin	skin_eQTL
rs9450302	SNHG5	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 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	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
3	chr6:86265600-86289800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:86266400-86290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:86272000-86290200	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:86278200-86302600	Weak transcription	Ovary	ovary
7	chr6:86278400-86291400	Weak transcription	Adipose Nuclei	Adipose
8	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:86280200-86290200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
11	chr6:86281600-86290000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:86281600-86290000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:86281600-86290200	Weak transcription	GM12878-XiMat	blood
14	chr6:86281600-86291800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:86281800-86290400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:86282200-86290400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:86282200-86291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:86282400-86290200	Weak transcription	Placenta	Placenta
19	chr6:86283000-86290200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:86283600-86290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:86284400-86292000	Enhancers	Stomach Mucosa	stomach
22	chr6:86285000-86290400	Weak transcription	Small Intestine	intestine
23	chr6:86285200-86290200	Weak transcription	Aorta	Aorta
24	chr6:86285400-86290400	Weak transcription	Hela-S3	cervix
25	chr6:86285600-86290000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:86285600-86290200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:86285600-86290200	Weak transcription	HSMM	muscle
28	chr6:86285600-86290600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:86285600-86290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:86286000-86291200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr6:86286400-86289800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:86286400-86290200	Weak transcription	Osteobl	bone
33	chr6:86286400-86290400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:86286400-86291200	Weak transcription	Brain Germinal Matrix	brain
35	chr6:86286600-86290400	Weak transcription	HUVEC	blood vessel
36	chr6:86286600-86291400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:86286600-86291600	Weak transcription	Brain Anterior Caudate	brain
38	chr6:86286600-86291600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:86286800-86289800	Weak transcription	NHDF-Ad	bronchial
41	chr6:86286800-86290800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:86286800-86297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:86287200-86291000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:86287400-86291200	Enhancers	Liver	Liver
45	chr6:86287600-86290000	Enhancers	Brain Hippocampus Middle	brain
46	chr6:86287600-86290400	Strong transcription	NHEK	skin
47	chr6:86287800-86290200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr6:86287800-86290400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr6:86287800-86291600	Weak transcription	Primary B cells from cord blood	blood
50	chr6:86288000-86289800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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