Variant report

Variant	rs4730988
Chromosome Location	chr7:120683751-120683752
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120590626..120592952-chr7:120680967..120683892,2	K562	blood:
2	chr7:120660852..120665277-chr7:120680137..120683898,4	K562	blood:
3	chr7:120683620..120687088-chr7:120702557..120704732,3	K562	blood:
4	chr7:120682952..120685567-chr7:120708911..120710433,2	K562	blood:
5	chr7:120682875..120684877-chr7:120691015..120693627,2	K562	blood:
6	chr7:120631348..120633454-chr7:120680148..120684056,4	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10085563	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224864	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233922	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12706310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986767	0.99[ASN][1000 genomes]
rs2013087	0.84[CEU][hapmap]
rs2074577	0.85[CEU][hapmap]
rs2110276	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2160010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160011	1.00[ASN][1000 genomes]
rs2160012	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2538485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2538487	1.00[ASN][1000 genomes]
rs2721325	1.00[ASN][1000 genomes]
rs2721326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2721336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2721337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2721340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2721345	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2896299	0.84[CEU][hapmap]
rs2908570	0.99[ASN][1000 genomes]
rs41688	0.85[CEU][hapmap]
rs4727915	0.84[CEU][hapmap]
rs4727917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730985	0.83[CEU][hapmap]
rs4730991	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965415	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794369	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808535	0.84[CEU][hapmap]
rs7808593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1031282	chr7:120667937-120887301	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv539099	chr7:120667937-120887301	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019025	chr7:120667937-120918696	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv539100	chr7:120667937-120918696	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv534342	chr7:120667938-120887300	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv889118	chr7:120683751-120800837	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4730988	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120673200-120685200	Weak transcription	Left Ventricle	heart
2	chr7:120673400-120689200	Weak transcription	HSMMtube	muscle
3	chr7:120673800-120694200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:120679200-120685200	Weak transcription	Aorta	Aorta
5	chr7:120680600-120685200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:120681600-120684400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr7:120681800-120684200	Transcr. at gene 5' and 3'	K562	blood
8	chr7:120682000-120683800	Enhancers	Ovary	ovary
9	chr7:120682000-120685200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:120682000-120687000	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:120682000-120689200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:120682000-120689400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:120682000-120689400	Weak transcription	Osteobl	bone
14	chr7:120682200-120687000	Weak transcription	Adipose Nuclei	Adipose
15	chr7:120682200-120687000	Weak transcription	NHDF-Ad	bronchial
16	chr7:120682200-120687600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:120682200-120695800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:120682400-120685600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:120682400-120687000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:120682400-120687000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:120682400-120688000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:120682400-120719600	Weak transcription	Fetal Lung	lung
23	chr7:120682600-120685400	Weak transcription	Hela-S3	cervix
24	chr7:120682600-120692000	Weak transcription	Fetal Stomach	stomach
25	chr7:120682800-120700800	Weak transcription	Fetal Kidney	kidney
26	chr7:120683000-120684200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr7:120683000-120686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:120683200-120687000	Weak transcription	HSMM	muscle
29	chr7:120683200-120689400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:120683200-120689400	Weak transcription	Right Ventricle	heart
31	chr7:120683400-120684200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr7:120683600-120683800	Enhancers	Psoas Muscle	Psoas
33	chr7:120683600-120683800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr7:120683600-120684400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr7:120683600-120684400	Enhancers	NHLF	lung
36	chr7:120683600-120687200	Enhancers	Liver	Liver

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