Variant report

Variant	rs12212560
Chromosome Location	chr6:86342679-86342680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
2	chr6:86325842..86327859-chr6:86341248..86343719,3	K562	blood:
3	chr6:86342168..86343867-chr6:86346506..86348145,2	MCF-7	breast:
4	chr6:86341603..86343165-chr6:86387354..86389820,2	K562	blood:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1059306	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs1059307	0.91[CEU][hapmap];0.81[MEX][hapmap]
rs10806334	0.80[EUR][1000 genomes]
rs10944128	0.87[CEU][hapmap];0.83[CHD][hapmap]
rs10944133	0.86[EUR][1000 genomes]
rs1173415	0.82[EUR][1000 genomes]
rs1173417	0.87[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1173418	0.88[CEU][hapmap]
rs12199873	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12203963	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs12205013	0.84[EUR][1000 genomes]
rs2475790	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2475791	0.86[EUR][1000 genomes]
rs2475792	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2758840	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2758842	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758843	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2758844	0.84[EUR][1000 genomes]
rs2758845	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2758846	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2758847	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2758848	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2758849	0.80[EUR][1000 genomes]
rs2783171	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2842600	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap]
rs2842601	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2842602	0.84[EUR][1000 genomes]
rs2842603	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842604	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842607	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842608	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842609	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842611	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2842612	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2842613	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842614	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842617	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087978	0.95[CEU][hapmap]
rs3812133	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs4145082	0.82[EUR][1000 genomes]
rs4304137	0.87[CEU][hapmap]
rs4348284	0.96[CEU][hapmap]
rs4351223	0.87[CEU][hapmap]
rs4373337	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4431401	0.96[CEU][hapmap];0.81[CHD][hapmap]
rs4441928	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4593336	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4707211	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs6454471	0.87[CEU][hapmap]
rs6454472	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs6454473	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6909767	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922	0.87[CEU][hapmap]
rs6935918	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7452605	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs7742201	0.86[CEU][hapmap]
rs7742691	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752502	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7757864	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762321	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7766485	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[MEX][hapmap]
rs7771612	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775864	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs911927	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294337	0.87[CEU][hapmap]
rs9342041	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9344532	0.82[CEU][hapmap]
rs9344533	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9344542	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9351065	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs9353318	0.87[CEU][hapmap]
rs9353320	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9353327	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9359658	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362230	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9362233	0.86[EUR][1000 genomes]
rs9444352	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs9450282	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs9450285	0.96[CEU][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs9450287	0.82[ASN][1000 genomes]
rs9450288	0.83[CHB][hapmap];0.81[MEX][hapmap]
rs9450302	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]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12212560	SNHG5	cis	Whole Blood	GTEx
rs12212560	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs12212560	SNHG5	cis	multi-tissue	Pritchard
rs12212560	SNHG5	cis	lymphoblastoid	seeQTL
rs12212560	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12212560	C6orf160	cis	uninvolved skin	skin_eQTL
rs12212560	SNHG5	cis	Artery Aorta	GTEx
rs12212560	C6orf160	cis	lesional skin	skin_eQTL
rs12212560	SNHG5	cis	Heart Left Ventricle	GTEx
rs12212560	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12212560	SNHG5	cis	Thyroid	GTEx
rs12212560	SNHG5	cis	Esophagus Mucosa	GTEx
rs12212560	SNHG5	cis	Esophagus Muscularis	GTEx
rs12212560	SNHG5	cis	Artery Tibial	GTEx
rs12212560	C6orf160	cis	normal skin	skin_eQTL
rs12212560	SNHG5	cis	Nerve Tibial	GTEx
rs12212560	SNHG5	cis	Muscle Skeletal	GTEx
rs12212560	SNHG5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
5	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
9	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
14	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
20	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:86319400-86348600	Strong transcription	K562	blood
22	chr6:86319600-86348200	Strong transcription	NHEK	skin
23	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:86320000-86348600	Strong transcription	Liver	Liver
27	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr6:86321000-86348600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:86323600-86349000	Strong transcription	Fetal Intestine Large	intestine
31	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:86324800-86348600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:86325400-86347000	Strong transcription	Hela-S3	cervix
34	chr6:86326400-86349200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:86331400-86348400	Strong transcription	NHDF-Ad	bronchial
37	chr6:86331400-86349000	Strong transcription	HSMM	muscle
38	chr6:86331600-86347400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:86331800-86347600	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr6:86332200-86346600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:86332400-86349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:86333400-86347200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr6:86335000-86346200	Strong transcription	Fetal Stomach	stomach
44	chr6:86335000-86348200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:86335200-86346000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:86335200-86349600	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:86335400-86343800	Strong transcription	HSMMtube	muscle
48	chr6:86335600-86345800	Strong transcription	Colonic Mucosa	Colon
49	chr6:86335600-86348200	Strong transcription	Fetal Lung	lung
50	chr6:86335600-86349000	Strong transcription	Adipose Nuclei	Adipose

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