Variant report

Variant	rs996903
Chromosome Location	chr7:120465559-120465560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120465079..120466716-chr7:120474858..120476670,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10225453	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10266755	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10272601	0.81[JPT][hapmap]
rs10274689	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10279837	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953922	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11982493	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669167	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673417	0.80[CEU][hapmap]
rs13231854	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17142976	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs17142995	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]
rs1859316	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1859319	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2040762	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074577	0.80[ASW][hapmap]
rs2097806	0.81[CHB][hapmap]
rs2107275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2189452	0.81[CHD][hapmap]
rs2244863	0.80[ASW][hapmap]
rs2248890	0.85[JPT][hapmap]
rs2524949	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2524951	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2525709	0.80[ASN][1000 genomes]
rs2525743	0.80[ASN][1000 genomes]
rs2721341	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2721343	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721347	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721354	0.87[ASW][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap]
rs2721364	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3735467	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757556	0.81[JPT][hapmap]
rs3779386	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3814460	0.84[ASN][1000 genomes]
rs3823859	0.93[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823861	0.80[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41611	0.86[ASN][1000 genomes]
rs41621	0.91[ASN][1000 genomes]
rs41623	0.81[CEU][hapmap]
rs41624	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs41627	0.91[ASN][1000 genomes]
rs41628	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs41629	0.88[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[ASN][1000 genomes]
rs41631	0.81[ASN][1000 genomes]
rs41632	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41690	0.80[ASW][hapmap]
rs4445165	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4730982	0.81[CEU][hapmap]
rs55855220	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61452531	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6466759	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466760	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466761	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466762	0.93[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67679138	0.80[EUR][1000 genomes]
rs6953454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958947	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6959328	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964344	0.81[JPT][hapmap]
rs6964667	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6964786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6979247	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs714259	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs727228	0.81[CHB][hapmap]
rs73427805	0.84[ASN][1000 genomes]
rs73427866	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs745167	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7781985	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7800318	0.82[ASN][1000 genomes]
rs7805211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7810542	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs996903	TSPAN12	cis	Artery Tibial	GTEx
rs996903	FLJ21986	cis	multi-tissue	Pritchard
rs996903	TSPAN12	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
3	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:120432600-120468400	Weak transcription	Lung	lung
5	chr7:120439400-120469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:120446000-120476200	Weak transcription	Left Ventricle	heart
9	chr7:120447400-120471400	Weak transcription	Fetal Kidney	kidney
10	chr7:120447800-120465600	Weak transcription	Liver	Liver
11	chr7:120449800-120476000	Weak transcription	HUVEC	blood vessel
12	chr7:120450600-120470400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:120452800-120476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:120455000-120465800	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:120455000-120467800	Weak transcription	Fetal Heart	heart
16	chr7:120455600-120468400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:120455600-120472200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:120455800-120465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:120455800-120474400	Weak transcription	Fetal Intestine Large	intestine
20	chr7:120455800-120476000	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:120458200-120468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:120458400-120475800	Weak transcription	Fetal Intestine Small	intestine
23	chr7:120460400-120469400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:120464000-120476000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:120464200-120465600	Weak transcription	Fetal Lung	lung
26	chr7:120465000-120465600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr7:120465000-120466400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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