Variant report

Variant	rs2058501
Chromosome Location	chr7:120680236-120680237
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:120597607..120599644-chr7:120678878..120681587,2	K562	blood:
2	chr7:120677015..120682377-chr7:120716797..120724177,13	K562	blood:
3	chr7:120655377..120657745-chr7:120679819..120681378,2	K562	blood:
4	chr7:120670213..120673148-chr7:120677345..120680325,2	K562	blood:
5	chr7:120649401..120651569-chr7:120679058..120681900,2	K562	blood:
6	chr7:120677155..120680507-chr7:120717086..120719349,5	K562	blood:
7	chr7:120660852..120665277-chr7:120680137..120683898,4	K562	blood:
8	chr7:120680122..120681952-chr7:120727272..120728827,2	K562	blood:
9	chr7:120679133..120681952-chr7:120727327..120728862,2	K562	blood:
10	chr7:120631348..120633454-chr7:120680148..120684056,4	K562	blood:
11	chr7:120679478..120681225-chr7:120714393..120716184,2	K562	blood:
12	chr7:120644958..120648520-chr7:120680179..120682620,4	K562	blood:
13	chr7:120673145..120676419-chr7:120676732..120680540,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10245811	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10245939	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10257314	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10277935	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1080807	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953923	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1118142	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11976117	0.82[CHB][hapmap]
rs12706305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17535702	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1981711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2074577	0.80[ASW][hapmap];0.96[LWK][hapmap]
rs2244863	0.80[ASW][hapmap]
rs2721341	0.93[LWK][hapmap]
rs2721354	0.81[LWK][hapmap]
rs3823859	0.80[ASW][hapmap]
rs41690	0.80[ASW][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap]
rs6466762	0.80[ASW][hapmap]
rs6944789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949989	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6956237	0.85[EUR][1000 genomes]
rs6958635	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6960415	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7781985	0.80[ASW][hapmap]
rs7782014	0.82[CHB][hapmap]
rs7782552	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7802570	0.82[CHB][hapmap]
rs7802665	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2058501	TSPAN12	cis	Artery Tibial	GTEx
rs2058501	NDUFA5	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120666600-120683600	Weak transcription	Liver	Liver
2	chr7:120670400-120681600	Weak transcription	HSMM	muscle
3	chr7:120673200-120681600	Weak transcription	Fetal Stomach	stomach
4	chr7:120673200-120685200	Weak transcription	Left Ventricle	heart
5	chr7:120673400-120681400	Weak transcription	NHDF-Ad	bronchial
6	chr7:120673400-120681600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:120673400-120681600	Weak transcription	Ovary	ovary
8	chr7:120673400-120689200	Weak transcription	HSMMtube	muscle
9	chr7:120673800-120694200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:120677400-120680600	Transcr. at gene 5' and 3'	K562	blood
11	chr7:120678800-120681800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr7:120679000-120681600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:120679000-120681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:120679000-120682200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:120679000-120683000	Weak transcription	Psoas Muscle	Psoas
16	chr7:120679200-120681600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:120679200-120685200	Weak transcription	Aorta	Aorta
18	chr7:120679400-120681600	Weak transcription	NHLF	lung
19	chr7:120679600-120681400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:120679600-120681600	Weak transcription	Adipose Nuclei	Adipose
21	chr7:120679600-120681600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:120680000-120680600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:120680200-120681600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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