Variant report

Variant	rs7953949
Chromosome Location	chr12:120687935-120687936
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:120687933-120687986	HUVEC	blood vessel:	n/a	n/a
2	USF1	chr12:120687625-120687997	A549	lung:	n/a	n/a
3	STAT3	chr12:120687817-120687947	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:120687079-120688316	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:120687807-120688056	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:120687550-120688256	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:120687791-120688098	HUVEC	blood vessel:	n/a	n/a
8	ZNF263	chr12:120687687-120687973	HEK293-T-REx	kidney:	n/a	n/a
9	POLR2A	chr12:120686890-120688841	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr12:120684586-120688694	PANC-1	pancreas:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
2	chr12:120684888..120687057-chr12:120687063..120691406,4	MCF-7	breast:
3	chr12:120684404..120691478-chr12:120697984..120705218,14	MCF-7	breast:
4	chr12:120685214..120692467-chr12:120727115..120732311,17	K562	blood:
5	chr12:120685626..120692224-chr12:120727115..120732105,16	K562	blood:
6	chr12:120686832..120689716-chr12:120699360..120703521,4	K562	blood:
7	chr12:120687678..120692479-chr12:120701581..120703521,4	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000240925	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10849739	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065064	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151824	0.98[EUR][1000 genomes]
rs1151825	0.98[EUR][1000 genomes]
rs1151827	0.98[EUR][1000 genomes]
rs1151830	0.94[EUR][1000 genomes]
rs1151832	0.98[EUR][1000 genomes]
rs1151837	0.98[EUR][1000 genomes]
rs1182860	0.98[EUR][1000 genomes]
rs11831552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1183781	0.98[EUR][1000 genomes]
rs12164847	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12305146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12308431	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12321884	0.86[AMR][1000 genomes]
rs12581983	0.87[AMR][1000 genomes]
rs1634814	0.98[EUR][1000 genomes]
rs1634815	0.98[EUR][1000 genomes]
rs2006194	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238156	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239208	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283364	0.86[AMR][1000 genomes]
rs2283365	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2524391	0.95[EUR][1000 genomes]
rs3759397	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3888587	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3888588	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3890165	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3956833	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61198412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300273	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs739809	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7966099	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120665200-120692000	Enhancers	Placenta	Placenta
2	chr12:120676400-120699400	Weak transcription	Aorta	Aorta
3	chr12:120682000-120689000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:120683200-120694800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:120683200-120695200	Weak transcription	Fetal Brain Male	brain
6	chr12:120684000-120692000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:120684600-120688400	Enhancers	Pancreas	Pancrea
8	chr12:120684600-120690600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:120684800-120688200	Enhancers	Fetal Muscle Trunk	muscle
10	chr12:120684800-120688600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:120685000-120688400	Enhancers	Brain Hippocampus Middle	brain
12	chr12:120685000-120688600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:120685000-120688600	Enhancers	Fetal Heart	heart
14	chr12:120685000-120688800	Genic enhancers	Fetal Intestine Small	intestine
15	chr12:120685000-120690600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:120685200-120688400	Enhancers	Brain Cingulate Gyrus	brain
17	chr12:120685200-120688600	Genic enhancers	Hela-S3	cervix
18	chr12:120685200-120688800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:120685200-120689000	Enhancers	K562	blood
20	chr12:120685400-120688400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:120685400-120688400	Enhancers	Esophagus	oesophagus
22	chr12:120685400-120689600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:120685400-120690400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:120685400-120691200	Enhancers	Spleen	Spleen
25	chr12:120685800-120688200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:120685800-120688600	Enhancers	Fetal Intestine Large	intestine
27	chr12:120686000-120688000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:120686000-120688000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:120686000-120688600	Enhancers	Brain Substantia Nigra	brain
30	chr12:120686000-120688800	Enhancers	Osteobl	bone
31	chr12:120686000-120689200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr12:120686000-120691000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:120686000-120700200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:120686200-120688000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:120686200-120688000	Weak transcription	Small Intestine	intestine
36	chr12:120686200-120688200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:120686200-120688800	Genic enhancers	NHLF	lung
38	chr12:120686400-120688000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:120686400-120688000	Enhancers	Gastric	stomach
40	chr12:120686400-120688800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:120686400-120688800	Enhancers	Lung	lung
42	chr12:120686400-120689400	Enhancers	Fetal Stomach	stomach
43	chr12:120686600-120688800	Genic enhancers	A549	lung
44	chr12:120686600-120690200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr12:120686600-120692800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:120686600-120693200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:120686600-120695000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:120686800-120688600	Enhancers	Fetal Lung	lung
49	chr12:120687000-120688000	Flanking Active TSS	Left Ventricle	heart
50	chr12:120687000-120688200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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