Variant report

Variant	rs17142976
Chromosome Location	chr7:120458978-120458979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120457286..120459639-chr7:120460525..120462886,2	K562	blood:
2	chr7:120454100..120457036-chr7:120458854..120461460,2	K562	blood:
3	chr7:120457748..120459607-chr7:120472145..120474237,2	K562	blood:
4	chr7:120458622..120460616-chr7:120461070..120463275,2	MCF-7	breast:
5	chr7:120452971..120457036-chr7:120458854..120462116,5	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10225453	0.85[CEU][hapmap]
rs10274689	0.95[CEU][hapmap]
rs114420	0.93[ASN][1000 genomes]
rs11976580	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs12154976	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs12669167	0.80[EUR][1000 genomes]
rs12673417	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132731	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs17142995	0.84[CEU][hapmap]
rs17143001	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs17143009	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs17143013	0.93[ASN][1000 genomes]
rs2189974	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2525706	0.81[ASN][1000 genomes]
rs2525710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2721329	0.81[ASN][1000 genomes]
rs2721330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2721332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2721344	0.93[ASN][1000 genomes]
rs2721346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs2721348	0.93[ASN][1000 genomes]
rs2721360	0.93[ASN][1000 genomes]
rs2721371	0.93[ASN][1000 genomes]
rs3823859	0.85[CEU][hapmap]
rs3823861	0.82[CEU][hapmap]
rs41613	1.00[ASN][1000 genomes]
rs41616	1.00[ASN][1000 genomes]
rs41617	1.00[ASN][1000 genomes]
rs41622	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41623	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41624	0.82[CEU][hapmap]
rs41626	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41632	0.82[CEU][hapmap]
rs42333	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4730982	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55733320	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55749650	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56023697	0.93[ASN][1000 genomes]
rs56067931	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61481874	0.93[ASN][1000 genomes]
rs6466759	0.85[CEU][hapmap]
rs6466760	0.85[CEU][hapmap]
rs6466761	0.85[CEU][hapmap]
rs6466762	0.85[CEU][hapmap]
rs67679138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953454	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs6959328	0.85[CEU][hapmap]
rs73427862	0.81[EUR][1000 genomes]
rs73427871	0.93[ASN][1000 genomes]
rs73427873	0.93[ASN][1000 genomes]
rs73427878	0.93[ASN][1000 genomes]
rs73721472	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7781985	0.86[CEU][hapmap]
rs7805733	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810542	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886440	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs996903	0.95[CEU][hapmap];0.80[EUR][1000 genomes]

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
rs17142976	TSPAN12	cis	parietal	SCAN
rs17142976	SPAM1	cis	cerebellum	SCAN
rs17142976	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 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	chr7:120446800-120462200	Weak transcription	GM12878-XiMat	blood
10	chr7:120447400-120471400	Weak transcription	Fetal Kidney	kidney
11	chr7:120447800-120465600	Weak transcription	Liver	Liver
12	chr7:120449800-120476000	Weak transcription	HUVEC	blood vessel
13	chr7:120450600-120470400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:120452800-120476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:120455000-120465800	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:120455000-120467800	Weak transcription	Fetal Heart	heart
17	chr7:120455600-120468400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:120455600-120472200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:120455800-120465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:120455800-120474400	Weak transcription	Fetal Intestine Large	intestine
21	chr7:120455800-120476000	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:120457800-120459000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:120458000-120462000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:120458200-120468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:120458400-120460000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:120458400-120475800	Weak transcription	Fetal Intestine Small	intestine

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