Variant report

Variant	rs2721340
Chromosome Location	chr7:120694229-120694230
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:120692179..120694802-chr7:120701783..120703966,2	K562	blood:
2	chr7:120692006..120694534-chr7:120721905..120723814,2	K562	blood:
3	chr7:120688479..120691904-chr7:120692456..120696539,4	K562	blood:
4	chr7:120692653..120696514-chr7:120719994..120724840,4	K562	blood:
5	chr7:120693988..120695530-chr7:120712060..120713807,2	K562	blood:
6	chr7:120692726..120696134-chr7:120727225..120730666,4	K562	blood:
7	chr7:120693342..120696134-chr7:120727225..120728840,2	K562	blood:
8	chr7:120662342..120664104-chr7:120692798..120695619,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction
ENSG00000234927	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10085563	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224864	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233922	0.97[ASN][1000 genomes]
rs12706307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12706308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12706310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986767	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];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];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2160010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160011	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160012	0.80[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538487	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538491	0.84[YRI][hapmap]
rs2721325	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721345	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721349	0.84[YRI][hapmap]
rs2896299	0.84[CEU][hapmap]
rs2908570	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];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];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730985	0.83[CEU][hapmap]
rs4730988	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]
rs4730991	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965415	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794369	0.80[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];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	nsv889119	chr7:120688463-120800837	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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
14	nsv889120	chr7:120691417-120800837	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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2721340	TSPAN12	cis	Artery Tibial	GTEx
rs2721340	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120682200-120695800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:120682400-120719600	Weak transcription	Fetal Lung	lung
3	chr7:120682800-120700800	Weak transcription	Fetal Kidney	kidney
4	chr7:120687800-120706600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:120689600-120709400	Weak transcription	HSMMtube	muscle
6	chr7:120689800-120698200	Weak transcription	Spleen	Spleen
7	chr7:120690200-120696200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:120690200-120709000	Weak transcription	Right Ventricle	heart
9	chr7:120690200-120709400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:120690400-120704200	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:120690400-120704400	Weak transcription	NHDF-Ad	bronchial
12	chr7:120690400-120709000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:120690600-120709200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:120691200-120696200	Weak transcription	NHLF	lung
15	chr7:120691200-120702000	Weak transcription	Liver	Liver
16	chr7:120691200-120703400	Weak transcription	Aorta	Aorta
17	chr7:120691200-120709000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:120692200-120695000	Strong transcription	HSMM	muscle
19	chr7:120692600-120698200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:120692800-120719000	Weak transcription	Left Ventricle	heart
21	chr7:120693000-120702000	Weak transcription	Ovary	ovary
22	chr7:120693000-120704400	Weak transcription	Fetal Stomach	stomach
23	chr7:120693400-120695200	Genic enhancers	K562	blood
24	chr7:120693400-120704200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr7:120694000-120695000	Enhancers	Skeletal Muscle Male	skeletal muscle

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