Variant report

Variant	rs17142995
Chromosome Location	chr7:120486797-120486798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10225453	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10252911	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10257297	0.81[ASN][1000 genomes]
rs10257475	0.81[ASN][1000 genomes]
rs10266755	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10272601	0.82[JPT][hapmap]
rs10274689	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279837	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953922	0.85[ASN][1000 genomes]
rs11982493	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12669167	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13231854	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557857	0.84[ASN][1000 genomes]
rs17132716	0.80[ASN][1000 genomes]
rs17142976	0.84[CEU][hapmap]
rs17143001	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs17143009	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1859316	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1859318	0.84[ASN][1000 genomes]
rs1859319	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2040762	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2097806	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs2107275	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107276	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2248890	0.80[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2524949	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2524951	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2525705	0.84[ASN][1000 genomes]
rs2525709	0.85[ASN][1000 genomes]
rs2525743	0.85[ASN][1000 genomes]
rs2721339	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2721341	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2721343	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2721347	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2721354	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2721364	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3735467	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757556	0.82[JPT][hapmap]
rs3779386	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3814460	0.89[ASN][1000 genomes]
rs3823859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823861	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41611	0.81[ASN][1000 genomes]
rs41621	0.87[ASN][1000 genomes]
rs41622	0.84[CEU][hapmap]
rs41624	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs41627	0.86[ASN][1000 genomes]
rs41628	0.86[ASN][1000 genomes]
rs41629	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs41632	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4445165	0.88[ASN][1000 genomes]
rs55855220	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61452531	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6466759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466760	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953454	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6958947	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959328	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6964344	0.81[JPT][hapmap]
rs6964667	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964786	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6971854	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6979247	0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs714259	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73427805	0.88[ASN][1000 genomes]
rs73427862	0.81[ASN][1000 genomes]
rs73427866	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73429803	0.81[ASN][1000 genomes]
rs73721472	0.80[EUR][1000 genomes]
rs745167	0.85[ASN][1000 genomes]
rs7776721	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7781985	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800318	0.87[ASN][1000 genomes]
rs7805211	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7805733	0.84[CEU][hapmap]
rs7810542	0.95[CEU][hapmap]
rs9649429	0.81[ASN][1000 genomes]
rs996903	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17142995	TSPAN12	cis	Artery Tibial	GTEx
rs17142995	TSPAN12	cis	Esophagus Muscularis	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:120468600-120487600	Weak transcription	Lung	lung
4	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
5	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:120476600-120492400	Weak transcription	Gastric	stomach
8	chr7:120477000-120489800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:120477000-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
11	chr7:120478400-120487400	Weak transcription	Colonic Mucosa	Colon
12	chr7:120479400-120488000	Weak transcription	Right Atrium	heart
13	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
14	chr7:120480000-120488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:120482600-120495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:120482600-120496200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:120482800-120487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:120482800-120492200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:120482800-120496400	Weak transcription	Liver	Liver
20	chr7:120482800-120496400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:120482800-120496600	Weak transcription	Stomach Mucosa	stomach
22	chr7:120483400-120496200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:120483400-120496400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:120483600-120487600	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:120483600-120496600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:120485000-120488000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:120485000-120488600	Enhancers	Fetal Intestine Large	intestine
28	chr7:120485000-120493800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:120485200-120487000	Weak transcription	Left Ventricle	heart
30	chr7:120485200-120496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:120485200-120496200	Weak transcription	Fetal Stomach	stomach
32	chr7:120485200-120496600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:120485200-120496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:120485400-120489800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:120485400-120489800	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:120485400-120496400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:120485400-120496400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:120485600-120488200	Enhancers	Fetal Intestine Small	intestine
39	chr7:120485800-120487200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:120485800-120488000	Weak transcription	Small Intestine	intestine
41	chr7:120486000-120487200	Enhancers	Right Ventricle	heart
42	chr7:120486000-120487600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:120486200-120488200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:120486400-120487600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr7:120486600-120486800	Enhancers	Fetal Heart	heart
46	chr7:120486600-120487800	Enhancers	Adipose Nuclei	Adipose
47	chr7:120486600-120488400	Enhancers	Fetal Kidney	kidney

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