Variant report

Variant	rs4680305
Chromosome Location	chr3:156533403-156533404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:156533389-156533682	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:156533232-156535613	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr3:156533377-156536265	GM18505	blood:	n/a	n/a
4	KAP1	chr3:156533340-156534056	HEK293	kidney:	n/a	n/a
5	MAX	chr3:156533259-156535596	HCT-116	colon:	n/a	n/a
6	BCLAF1	chr3:156533294-156536171	GM12878	blood:	n/a	chr3:156534858-156534867 chr3:156533900-156533913 chr3:156535653-156535662 chr3:156534856-156534869
7	POLR2A	chr3:156533374-156536410	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr3:156533326-156536205	GM19099	blood:	n/a	n/a
9	POLR2A	chr3:156533397-156536445	GM12892	blood:	n/a	n/a
10	MTA3	chr3:156533243-156536326	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:156532815-156536469	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:156533252-156537169	IMR90	lung:	n/a	n/a
13	ZNF384	chr3:156533149-156533544	GM12878	blood:	n/a	n/a
14	PML	chr3:156533298-156536576	GM12878	blood:	n/a	chr3:156535424-156535433
15	POLR2A	chr3:156533254-156536323	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:156533398-156534317	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr3:156533087-156536490	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156426710..156429156-chr3:156532890..156534786,2	MCF-7	breast:
2	chr3:156530292..156533416-chr3:156536221..156538650,3	MCF-7	breast:
3	chr3:156270408..156273288-chr3:156530835..156533779,2	MCF-7	breast:
4	chr3:156531546..156534096-chr3:156793933..156795686,2	MCF-7	breast:
5	chr3:156400050..156402088-chr3:156531912..156534314,2	MCF-7	breast:
6	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
7	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
8	chr3:156402796..156405445-chr3:156530779..156533531,2	MCF-7	breast:
9	chr3:156409514..156412147-chr3:156532498..156534140,2	K562	blood:
10	chr3:156532344..156534533-chr3:156884722..156886636,3	MCF-7	breast:
11	chr3:156517343..156519280-chr3:156530527..156533564,3	MCF-7	breast:
12	chr3:156256323..156258307-chr3:156531885..156534419,2	MCF-7	breast:
13	chr3:156533151..156536166-chr3:156876536..156878958,4	MCF-7	breast:
14	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-10	chr3:156533269-156533862	NONHSAT092868

No data

Variant related genes	Relation type
PA2G4P4	TF binding region
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10936037	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936038	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707914	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11711674	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717133	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492804	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492968	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12497539	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072896	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13086516	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097325	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430410	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430411	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560415	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560416	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1835372	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59717073	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776157	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7638625	0.81[EUR][1000 genomes]
rs7641929	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812169	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9818684	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9820830	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837271	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842198	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858861	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4680305	LINC00886	cis	Esophagus Mucosa	GTEx
rs4680305	LINC00886	cis	Adipose Subcutaneous	GTEx
rs4680305	LINC00886	cis	Esophagus Muscularis	GTEx
rs4680305	LINC00886	cis	Stomach	GTEx
rs4680305	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs4680305	LINC00886	cis	Thyroid	GTEx
rs4680305	LINC00886	cis	Artery Aorta	GTEx
rs4680305	LINC00886	cis	lung	GTEx
rs4680305	LINC00886	cis	Nerve Tibial	GTEx
rs4680305	LINC00886	cis	Artery Tibial	GTEx
rs4680305	LINC00886	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:156527800-156533800	Enhancers	HMEC	breast
3	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:156529200-156533600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:156529600-156533600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:156529800-156533600	Weak transcription	Fetal Heart	heart
7	chr3:156530600-156533600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156530600-156533800	Weak transcription	Lung	lung
9	chr3:156530800-156533800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:156530800-156533800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:156530800-156533800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:156530800-156533800	Weak transcription	Left Ventricle	heart
13	chr3:156531000-156533600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:156531000-156533600	Weak transcription	HSMMtube	muscle
15	chr3:156531000-156533800	Weak transcription	Right Ventricle	heart
16	chr3:156531000-156533800	Weak transcription	Small Intestine	intestine
17	chr3:156531200-156533600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:156531200-156533600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:156531200-156533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:156531200-156533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:156531200-156533600	Weak transcription	Osteobl	bone
22	chr3:156531200-156533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:156531200-156533800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:156531200-156533800	Weak transcription	Esophagus	oesophagus
25	chr3:156531200-156533800	Weak transcription	Pancreas	Pancrea
26	chr3:156531200-156533800	Weak transcription	Psoas Muscle	Psoas
27	chr3:156531200-156533800	Weak transcription	Right Atrium	heart
28	chr3:156531200-156533800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:156531200-156533800	Weak transcription	HSMM	muscle
30	chr3:156531200-156534000	Weak transcription	Aorta	Aorta
31	chr3:156531200-156534000	Weak transcription	Gastric	stomach
32	chr3:156531200-156534200	Weak transcription	Stomach Mucosa	stomach
33	chr3:156531400-156533600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:156531400-156534000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:156531400-156534600	Weak transcription	K562	blood
36	chr3:156531600-156533600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:156531600-156533800	Active TSS	GM12878-XiMat	blood
38	chr3:156531800-156534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:156532400-156533800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:156532800-156533800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:156533000-156533600	Enhancers	Fetal Intestine Large	intestine
42	chr3:156533000-156533600	Enhancers	Hela-S3	cervix
43	chr3:156533000-156534200	Bivalent Enhancer	Fetal Brain Male	brain
44	chr3:156533200-156533600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr3:156533200-156533800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:156533200-156533800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr3:156533200-156533800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr3:156533200-156534200	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr3:156533200-156535400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr3:156533200-156536200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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