Variant report

Variant	rs10953923
Chromosome Location	chr7:120661851-120661852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120659278..120662150-chr7:120687240..120689583,2	K562	blood:
2	chr7:120660560..120662573-chr7:120715794..120718811,3	K562	blood:
3	chr7:120661476..120663248-chr7:120721625..120723394,2	K562	blood:
4	chr7:120660852..120665277-chr7:120680137..120683898,4	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10245811	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10245939	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10257314	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10277935	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1080807	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1118142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976117	0.82[CHB][hapmap]
rs12706305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706306	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17535702	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2058501	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]
rs2074577	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs2244863	0.80[ASW][hapmap];0.82[LWK][hapmap]
rs2721363	0.82[LWK][hapmap]
rs3823859	0.80[ASW][hapmap]
rs41690	0.80[ASW][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap]
rs6466761	0.80[ASW][hapmap]
rs6466762	0.80[ASW][hapmap]
rs6944789	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];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6949989	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6956237	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6958635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960415	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7781985	0.80[ASW][hapmap]
rs7782014	0.82[CHB][hapmap]
rs7782552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802570	0.82[CHB][hapmap]
rs7802665	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10953923	NDUFA5	cis	cerebellum	SCAN
rs10953923	TSPAN12	cis	Artery Tibial	GTEx
rs10953923	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
2	chr7:120649400-120663600	Weak transcription	Left Ventricle	heart
3	chr7:120652800-120663800	Weak transcription	Small Intestine	intestine
4	chr7:120653400-120663600	Weak transcription	Psoas Muscle	Psoas
5	chr7:120654800-120663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:120656000-120663600	Weak transcription	Ovary	ovary
7	chr7:120656000-120668000	Weak transcription	Right Atrium	heart
8	chr7:120657000-120663600	Enhancers	Hela-S3	cervix
9	chr7:120657800-120663600	Weak transcription	Aorta	Aorta
10	chr7:120657800-120666400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:120658000-120663600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:120658000-120665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:120659000-120662200	Enhancers	NHLF	lung
14	chr7:120659600-120663000	Weak transcription	Fetal Heart	heart
15	chr7:120659600-120663200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:120659800-120662000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:120659800-120662000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:120659800-120662000	Enhancers	HUVEC	blood vessel
19	chr7:120659800-120663800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:120660000-120662600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:120660400-120662400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:120660400-120664200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:120660600-120663200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr7:120660600-120663400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:120660800-120662600	Enhancers	Fetal Lung	lung
26	chr7:120660800-120663800	Enhancers	Rectal Smooth Muscle	rectum
27	chr7:120660800-120665000	Enhancers	Liver	Liver
28	chr7:120660800-120665200	Enhancers	Colon Smooth Muscle	Colon
29	chr7:120661000-120662200	Enhancers	Fetal Kidney	kidney
30	chr7:120661000-120663600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:120661000-120668000	Weak transcription	HSMMtube	muscle
32	chr7:120661200-120663200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:120661200-120664000	Weak transcription	NH-A	brain
34	chr7:120661400-120662000	Enhancers	Fetal Stomach	stomach
35	chr7:120661400-120664000	Strong transcription	HSMM	muscle
36	chr7:120661600-120663600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:120661600-120669400	Genic enhancers	K562	blood
38	chr7:120661800-120662000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr7:120661800-120662600	Weak transcription	NHDF-Ad	bronchial
40	chr7:120661800-120662800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:120661800-120663600	Weak transcription	Adipose Nuclei	Adipose
42	chr7:120661800-120663600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr7:120661800-120663600	Weak transcription	Osteobl	bone

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