Variant report

Variant	rs12199873
Chromosome Location	chr6:86294947-86294948
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86294224..86298589-chr6:86301078..86306001,4	MCF-7	breast:
2	chr6:86294695..86297402-chr6:86376038..86378724,2	K562	blood:
3	chr6:86294754..86298777-chr6:86299293..86305225,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1059306	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10944133	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10944137	0.82[CEU][hapmap]
rs1173415	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs11755642	0.82[CEU][hapmap]
rs12192546	0.82[CEU][hapmap]
rs12193904	0.82[CEU][hapmap]
rs12203963	0.84[CEU][hapmap]
rs12205013	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12212480	0.81[CEU][hapmap]
rs12212560	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs13207173	0.82[CEU][hapmap]
rs1335442	0.82[CEU][hapmap]
rs1885607	0.84[EUR][1000 genomes]
rs2065114	0.91[CHB][hapmap]
rs2225754	0.82[CEU][hapmap]
rs2229523	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2475790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2475791	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2475792	0.86[CEU][hapmap]
rs2484355	0.85[EUR][1000 genomes]
rs2758840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758842	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2758843	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2758844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758845	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2758846	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758848	0.83[CEU][hapmap]
rs2783171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842600	0.83[CEU][hapmap]
rs2842601	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842602	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842603	0.87[CEU][hapmap]
rs2842604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2842609	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2842611	0.83[CEU][hapmap]
rs2842612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842614	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2842617	0.86[EUR][1000 genomes]
rs3087978	0.83[CEU][hapmap]
rs3812133	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145082	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235826	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4235827	0.90[ASN][1000 genomes]
rs4304137	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4348284	0.84[CEU][hapmap]
rs4351223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4383777	0.81[EUR][1000 genomes]
rs4419647	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4431401	0.83[CEU][hapmap]
rs4441928	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4501401	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4579322	0.90[CHB][hapmap]
rs4706240	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707207	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4707209	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707211	0.84[CEU][hapmap]
rs4707217	0.84[EUR][1000 genomes]
rs6454469	0.83[ASN][1000 genomes]
rs6454471	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6454486	0.81[EUR][1000 genomes]
rs6454487	0.82[CEU][hapmap]
rs6909767	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926049	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7452605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742201	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs7742691	0.91[CEU][hapmap]
rs7746065	0.91[CHB][hapmap]
rs7768065	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770359	0.85[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7775864	0.86[EUR][1000 genomes]
rs911927	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9294337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9342041	0.87[EUR][1000 genomes]
rs9344532	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9344542	0.87[CEU][hapmap]
rs9351065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9353318	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353320	0.85[EUR][1000 genomes]
rs9353327	0.87[CEU][hapmap]
rs9359658	0.83[EUR][1000 genomes]
rs9362230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9362233	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9362239	0.82[EUR][1000 genomes]
rs9444349	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9444352	0.83[CEU][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	0.83[CEU][hapmap]
rs9450290	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9450318	0.82[EUR][1000 genomes]
rs9450319	0.81[EUR][1000 genomes]
rs9647601	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12199873	SNHG5	cis	Artery Tibial	GTEx
rs12199873	SNHG5	cis	Esophagus Muscularis	GTEx
rs12199873	SNHG5	cis	Whole Blood	GTEx
rs12199873	SNHG5	cis	Heart Left Ventricle	GTEx
rs12199873	C6orf160	cis	normal skin	skin_eQTL
rs12199873	SNHG5	cis	Esophagus Mucosa	GTEx
rs12199873	C6orf160	cis	uninvolved skin	skin_eQTL
rs12199873	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12199873	SNHG5	cis	Muscle Skeletal	GTEx
rs12199873	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs12199873	SNHG5	cis	Nerve Tibial	GTEx
rs12199873	SNHG5	cis	multi-tissue	Pritchard
rs12199873	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12199873	SNHG5	cis	Thyroid	GTEx
rs12199873	SNHG5	cis	lung	GTEx
rs12199873	C6orf160	cis	lesional skin	skin_eQTL

Chromatin state (count:61 , 50 per page) page: 1 2

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	chr6:86278200-86302600	Weak transcription	Ovary	ovary
4	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
6	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:86286800-86297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:86288200-86301400	Weak transcription	Fetal Heart	heart
9	chr6:86288400-86295600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:86288600-86295400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:86289200-86301000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:86289800-86297600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:86290000-86300800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:86290000-86301000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:86290200-86301800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:86290400-86301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
18	chr6:86290800-86295600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:86290800-86296400	Weak transcription	Fetal Stomach	stomach
20	chr6:86290800-86301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:86290800-86302000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:86291000-86295400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:86291000-86295600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:86291000-86296400	Weak transcription	Left Ventricle	heart
25	chr6:86291000-86296400	Weak transcription	Psoas Muscle	Psoas
26	chr6:86291000-86297000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:86291000-86297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:86291000-86297200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:86291000-86302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:86291000-86302000	Weak transcription	HSMM	muscle
31	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:86291200-86298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:86291200-86300600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:86291200-86301000	Weak transcription	Primary T cells from cord blood	blood
35	chr6:86291200-86301200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:86291200-86301200	Weak transcription	Hela-S3	cervix
37	chr6:86291200-86301200	Weak transcription	NHEK	skin
38	chr6:86291200-86301400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:86291200-86301800	Weak transcription	HUVEC	blood vessel
40	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
41	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:86291200-86302800	Weak transcription	Gastric	stomach
43	chr6:86291400-86300400	Weak transcription	A549	lung
44	chr6:86292000-86298600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:86292000-86299800	Weak transcription	HepG2	liver
46	chr6:86292000-86300400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:86292000-86300600	Weak transcription	K562	blood
48	chr6:86292000-86301000	Weak transcription	Primary B cells from cord blood	blood
49	chr6:86292000-86301200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:86292000-86301800	Weak transcription	NHDF-Ad	bronchial

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