Variant report

Variant	rs12203963
Chromosome Location	chr6:86223316-86223317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86216856..86218839-chr6:86222143..86224772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1059306	0.84[CEU][hapmap]
rs1059307	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs10944128	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10944129	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs1173418	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11752251	0.85[ASN][1000 genomes]
rs11752795	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191637	0.84[ASN][1000 genomes]
rs12193777	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12199873	0.84[CEU][hapmap]
rs12206573	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12212560	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs2475790	0.84[CEU][hapmap]
rs2475792	0.86[CEU][hapmap]
rs2758840	0.83[CEU][hapmap]
rs2758842	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs2758843	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2758845	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs2758847	0.83[CEU][hapmap]
rs2758848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2758849	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2783171	0.83[CEU][hapmap]
rs2842600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842601	0.83[CEU][hapmap]
rs2842603	0.88[CEU][hapmap];0.83[CHB][hapmap]
rs2842605	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842607	0.83[CEU][hapmap]
rs2842608	0.83[CEU][hapmap]
rs2842609	0.84[CEU][hapmap]
rs2842610	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842611	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]
rs2842612	0.82[CEU][hapmap]
rs2842613	0.83[CEU][hapmap]
rs2842614	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2842615	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3087978	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs34980280	0.89[EUR][1000 genomes]
rs4304137	0.84[CEU][hapmap]
rs4348284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4351223	0.83[CEU][hapmap]
rs4431401	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4640862	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707212	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454471	0.84[CEU][hapmap]
rs6454472	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909767	0.91[CEU][hapmap]
rs6922	0.83[CEU][hapmap]
rs6927475	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs7452605	0.83[CEU][hapmap]
rs7742691	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs7761762	0.81[EUR][1000 genomes]
rs7766485	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs7775864	0.86[CHB][hapmap]
rs911927	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs9294337	0.84[CEU][hapmap]
rs9342045	0.85[EUR][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs9344540	0.83[EUR][1000 genomes]
rs9344542	0.87[CEU][hapmap]
rs9351065	0.83[CEU][hapmap]
rs9353327	0.87[CEU][hapmap]
rs9362230	0.83[CEU][hapmap]
rs9362232	0.86[EUR][1000 genomes]
rs9444348	0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9444351	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444354	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450273	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9450277	0.81[ASN][1000 genomes]
rs9450284	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9450285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450288	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450292	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450302	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs9450311	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9885944	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
rs12203963	SNHG5	cis	Esophagus Muscularis	GTEx
rs12203963	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12203963	C6orf160	cis	uninvolved skin	skin_eQTL
rs12203963	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs12203963	SNHG5	cis	Stomach	GTEx
rs12203963	SNHG5	cis	Esophagus Mucosa	GTEx
rs12203963	SNHG5	cis	Artery Tibial	GTEx
rs12203963	SNHG5	cis	Nerve Tibial	GTEx
rs12203963	SNHG5	cis	Muscle Skeletal	GTEx
rs12203963	C6orf160	cis	normal skin	skin_eQTL
rs12203963	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12203963	SNHG5	cis	Thyroid	GTEx
rs12203963	SNHG5	cis	Heart Left Ventricle	GTEx
rs12203963	SNHG5	cis	Whole Blood	GTEx
rs12203963	SNHG5	cis	multi-tissue	Pritchard
rs12203963	SNHG5	cis	Artery Aorta	GTEx
rs12203963	C6orf160	cis	lesional skin	skin_eQTL
rs12203963	SNHG5	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
3	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
4	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
5	chr6:86211400-86246400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:86212000-86224800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:86212000-86228600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr6:86212000-86246600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:86214000-86225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:86215200-86224200	Strong transcription	NHDF-Ad	bronchial
11	chr6:86215800-86227600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:86216000-86225400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr6:86216200-86225600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:86216400-86224600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:86216400-86224800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:86217000-86224200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:86217000-86224600	Strong transcription	HSMM	muscle
18	chr6:86217400-86223400	Strong transcription	Left Ventricle	heart
19	chr6:86217600-86223400	Strong transcription	Fetal Intestine Large	intestine
20	chr6:86217600-86223400	Strong transcription	HSMMtube	muscle
21	chr6:86217600-86223800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:86217600-86224000	Strong transcription	Brain Anterior Caudate	brain
23	chr6:86217600-86224200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:86217600-86224200	Strong transcription	Placenta	Placenta
25	chr6:86217600-86224800	Strong transcription	Primary B cells from cord blood	blood
26	chr6:86217800-86224400	Strong transcription	Adipose Nuclei	Adipose
27	chr6:86218000-86224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:86218000-86260200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:86218400-86223600	Strong transcription	NH-A	brain
30	chr6:86218400-86224000	Strong transcription	Primary T cells from cord blood	blood
31	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:86218600-86223400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:86218600-86224400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:86218600-86226000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:86218800-86223400	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr6:86218800-86223400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:86218800-86224000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr6:86218800-86224400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr6:86218800-86224400	Strong transcription	Liver	Liver
40	chr6:86218800-86224600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr6:86219200-86223400	Strong transcription	Brain Hippocampus Middle	brain
42	chr6:86219200-86223400	Strong transcription	Fetal Kidney	kidney
43	chr6:86219200-86223400	Strong transcription	Fetal Lung	lung
44	chr6:86219200-86224000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:86219200-86224200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:86219200-86224200	Strong transcription	GM12878-XiMat	blood
47	chr6:86219200-86227600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:86219200-86246200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:86219400-86223400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:86219400-86223400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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