Variant report

Variant	rs10245939
Chromosome Location	chr7:120642598-120642599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120590021..120592843-chr7:120639404..120643575,5	K562	blood:
2	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
3	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000071243	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10257314	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10277935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1080807	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953923	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1118142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706305	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706306	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17535702	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981711	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058501	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244865	0.82[AFR][1000 genomes]
rs41690	0.82[AFR][1000 genomes]
rs6944789	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6949989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956237	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6958635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960415	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7782552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10245939	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120634200-120644000	Weak transcription	Spleen	Spleen
2	chr7:120637000-120646800	Weak transcription	Placenta	Placenta
3	chr7:120637200-120647000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
5	chr7:120638200-120643600	Weak transcription	Left Ventricle	heart
6	chr7:120638800-120643800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr7:120639000-120645000	Enhancers	Liver	Liver
8	chr7:120640000-120644800	Enhancers	Fetal Stomach	stomach
9	chr7:120640400-120644800	Genic enhancers	HSMM	muscle
10	chr7:120640600-120644000	Enhancers	NHLF	lung
11	chr7:120640600-120644200	Enhancers	Osteobl	bone
12	chr7:120640600-120644400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:120640800-120642600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:120640800-120643200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:120640800-120643200	Weak transcription	Aorta	Aorta
16	chr7:120640800-120643600	Weak transcription	Right Atrium	heart
17	chr7:120640800-120643800	Enhancers	Stomach Smooth Muscle	stomach
18	chr7:120640800-120644000	Enhancers	Adipose Nuclei	Adipose
19	chr7:120640800-120646000	Weak transcription	Brain Anterior Caudate	brain
20	chr7:120641000-120643600	Enhancers	NHDF-Ad	bronchial
21	chr7:120641400-120642600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr7:120641600-120643000	Weak transcription	Ovary	ovary
23	chr7:120641800-120643000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:120641800-120643200	Enhancers	Fetal Kidney	kidney
25	chr7:120641800-120643200	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:120641800-120644000	Enhancers	NH-A	brain
27	chr7:120642000-120642600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr7:120642000-120643000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:120642000-120643200	Weak transcription	Psoas Muscle	Psoas
30	chr7:120642000-120643600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:120642000-120645000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr7:120642000-120647000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:120642200-120642600	Transcr. at gene 5' and 3'	K562	blood
34	chr7:120642200-120642800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:120642200-120643200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:120642200-120643400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr7:120642200-120643400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:120642200-120643400	Enhancers	Fetal Heart	heart
39	chr7:120642200-120643400	Enhancers	HSMMtube	muscle
40	chr7:120642200-120643600	Enhancers	Fetal Lung	lung
41	chr7:120642200-120644800	Enhancers	Colon Smooth Muscle	Colon
42	chr7:120642400-120642600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:120642400-120642600	Enhancers	Stomach Mucosa	stomach
44	chr7:120642400-120642600	Bivalent Enhancer	HUVEC	blood vessel
45	chr7:120642400-120643000	Weak transcription	Hela-S3	cervix
46	chr7:120642400-120643200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:120642400-120644600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr7:120642400-120644600	Enhancers	Rectal Smooth Muscle	rectum

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