Variant report

Variant	rs6766480
Chromosome Location	chr3:196014073-196014074
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196012776..196015922-chr3:196063347..196066816,3	MCF-7	breast:
2	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:
3	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
4	chr3:195965458..195967733-chr3:196012588..196015404,2	MCF-7	breast:
5	chr3:196013567..196017227-chr3:196043342..196045325,4	MCF-7	breast:
6	chr3:196012669..196015162-chr3:196043820..196046764,2	K562	blood:
7	chr3:196013815..196016163-chr6:27090213..27092532,2	MCF-7	breast:
8	chr3:196012352..196016755-chr3:196062622..196069148,9	K562	blood:
9	chr14:20811412..20812021-chr3:196013817..196014529,2	Hela-S3	cervix:
10	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:
11	chr3:196013508..196016403-chr3:196043043..196046288,6	MCF-7	breast:
12	chr3:196013398..196015851-chr3:196068583..196071493,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272741	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000272468	Chromatin interaction
ENSG00000237418	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000259001	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000212146	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000129484	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11914521	0.97[ASN][1000 genomes]
rs11929532	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12497601	0.89[MKK][hapmap]
rs12629949	0.83[ASN][1000 genomes]
rs12633502	0.81[ASN][1000 genomes]
rs12634304	0.82[ASN][1000 genomes]
rs12637288	0.89[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12637379	0.97[ASN][1000 genomes]
rs1357289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948690	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2047550	0.88[CHB][hapmap];0.96[CHD][hapmap]
rs2047551	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2088666	0.89[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2270769	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2280526	0.84[MKK][hapmap]
rs2293160	0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3772109	0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4396926	0.84[ASN][1000 genomes]
rs4916421	0.89[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4916424	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916425	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916456	0.84[ASN][1000 genomes]
rs4916476	0.90[ASN][1000 genomes]
rs4916477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916479	0.89[ASN][1000 genomes]
rs4916485	0.88[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs55878253	0.97[ASN][1000 genomes]
rs55996879	0.83[ASN][1000 genomes]
rs56240083	0.97[ASN][1000 genomes]
rs56370923	0.97[ASN][1000 genomes]
rs58297632	0.84[ASN][1000 genomes]
rs59289255	0.81[ASN][1000 genomes]
rs59352354	0.84[ASN][1000 genomes]
rs60216585	0.97[ASN][1000 genomes]
rs60336404	0.97[ASN][1000 genomes]
rs66487782	0.84[ASN][1000 genomes]
rs66780758	0.84[ASN][1000 genomes]
rs66805306	0.84[ASN][1000 genomes]
rs66927787	0.84[ASN][1000 genomes]
rs66942309	0.81[ASN][1000 genomes]
rs67204670	0.81[ASN][1000 genomes]
rs67317524	0.97[ASN][1000 genomes]
rs67349960	0.84[ASN][1000 genomes]
rs67600689	0.97[ASN][1000 genomes]
rs6762272	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6777819	0.86[LWK][hapmap];0.90[MKK][hapmap]
rs67784045	0.84[ASN][1000 genomes]
rs6778879	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6785339	0.82[MKK][hapmap]
rs68056570	0.84[ASN][1000 genomes]
rs6809764	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72611188	0.83[ASN][1000 genomes]
rs73212155	0.90[ASN][1000 genomes]
rs73212160	0.97[ASN][1000 genomes]
rs73212178	0.81[ASN][1000 genomes]
rs7616433	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7631913	0.85[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap]
rs7636149	0.89[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7640304	0.84[ASN][1000 genomes]
rs9714038	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6766480	TM4SF19-AS1	cis	Muscle Skeletal	GTEx
rs6766480	MGC33212	cis	multi-tissue	Pritchard
rs6766480	TCTEX1D2	cis	parietal	SCAN
rs6766480	TM4SF19	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196012400-196014200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:196012400-196014200	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:196012400-196014400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr3:196012400-196014800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr3:196012400-196015400	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:196012400-196015600	Active TSS	HSMMtube	muscle
7	chr3:196012600-196014200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr3:196012600-196014200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:196012600-196015400	Active TSS	Colonic Mucosa	Colon
10	chr3:196012600-196015800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:196012800-196015600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:196013000-196014400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:196013000-196015400	Active TSS	NHLF	lung
14	chr3:196013000-196015600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:196013000-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:196013000-196015600	Active TSS	Small Intestine	intestine
17	chr3:196013200-196014200	Active TSS	Right Atrium	heart
18	chr3:196013200-196014200	Flanking Active TSS	Dnd41	blood
19	chr3:196013200-196015200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:196013200-196015200	Active TSS	Gastric	stomach
21	chr3:196013200-196015400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:196013200-196015400	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr3:196013200-196015600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:196013200-196015600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:196013200-196015600	Active TSS	Fetal Intestine Small	intestine
26	chr3:196013200-196015600	Active TSS	Left Ventricle	heart
27	chr3:196013200-196015600	Active TSS	Psoas Muscle	Psoas
28	chr3:196013200-196015600	Active TSS	Right Ventricle	heart
29	chr3:196013200-196015800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:196013400-196014200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:196013400-196014200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:196013400-196015400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:196013400-196015400	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr3:196013400-196015400	Active TSS	HMEC	breast
35	chr3:196013400-196015400	Active TSS	NHDF-Ad	bronchial
36	chr3:196013400-196015600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:196013400-196015600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr3:196013400-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:196013400-196015600	Active TSS	GM12878-XiMat	blood
40	chr3:196013400-196015600	Active TSS	K562	blood
41	chr3:196013400-196015800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:196013400-196015800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:196013400-196015800	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr3:196013400-196015800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:196013400-196015800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:196013400-196015800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:196013400-196015800	Active TSS	A549	lung
48	chr3:196013400-196015800	Active TSS	HSMM	muscle
49	chr3:196013400-196015800	Active TSS	NHEK	skin
50	chr3:196013400-196016000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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