Variant report

Variant	rs7871178
Chromosome Location	chr9:27148475-27148476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10967624	1.00[CHB][hapmap]
rs10967625	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10967634	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10967639	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10967640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10967734	0.94[ASN][1000 genomes]
rs1161603	1.00[CHB][hapmap]
rs11788136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12005388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12336187	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12337860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12339162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12340500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12343345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12349359	1.00[CHB][hapmap]
rs12350053	0.94[ASN][1000 genomes]
rs12350086	0.94[ASN][1000 genomes]
rs12352441	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12352603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12352631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12551926	0.81[ASN][1000 genomes]
rs12554485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13293051	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16911083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17694549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17694796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17756221	1.00[JPT][hapmap]
rs17756599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17756667	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17756685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2027124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs36090003	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs615532	1.00[CHB][hapmap]
rs62542752	0.94[ASN][1000 genomes]
rs62542753	0.94[ASN][1000 genomes]
rs62542755	0.94[ASN][1000 genomes]
rs62542757	0.94[ASN][1000 genomes]
rs62542758	0.94[ASN][1000 genomes]
rs62544592	0.94[ASN][1000 genomes]
rs62544593	0.94[ASN][1000 genomes]
rs62544597	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62544598	0.94[ASN][1000 genomes]
rs62544599	0.94[ASN][1000 genomes]
rs62544600	0.94[ASN][1000 genomes]
rs62544601	0.94[ASN][1000 genomes]
rs62544602	1.00[ASN][1000 genomes]
rs62544603	1.00[ASN][1000 genomes]
rs62544604	1.00[ASN][1000 genomes]
rs6475959	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6475960	0.94[ASN][1000 genomes]
rs6475962	0.84[ASN][1000 genomes]
rs6475963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6475964	0.94[ASN][1000 genomes]
rs6475965	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475966	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6475968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66704846	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66779473	0.94[ASN][1000 genomes]
rs67294931	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67322240	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67667821	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023335	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023443	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7024233	0.94[ASN][1000 genomes]
rs7037509	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7040772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042119	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043905	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7044842	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71510418	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7847161	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7847166	0.86[AFR][1000 genomes]
rs7847280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7854048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7862613	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7862757	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7873019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873161	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv613945	chr9:27121906-27148475	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv892863	chr9:27138898-27170934	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7871178	TEK	cis	cerebellum	SCAN
rs7871178	MOBKL2B	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27122800-27150800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:27143200-27150000	Weak transcription	Right Atrium	heart
3	chr9:27143800-27150200	Weak transcription	Fetal Lung	lung
4	chr9:27144000-27149800	Weak transcription	Lung	lung
5	chr9:27145000-27149600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:27145200-27149400	Weak transcription	Fetal Stomach	stomach
7	chr9:27145400-27149600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:27145400-27149600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:27145400-27149600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:27145400-27149600	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:27145400-27149600	Weak transcription	Left Ventricle	heart
12	chr9:27145400-27149600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:27145400-27149600	Weak transcription	Spleen	Spleen
14	chr9:27145400-27150200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:27145400-27150200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:27145400-27150200	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:27145400-27150400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:27145600-27149600	Weak transcription	HUVEC	blood vessel
19	chr9:27145600-27150000	Weak transcription	Adipose Nuclei	Adipose
20	chr9:27145600-27150600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:27145800-27150000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:27147800-27155000	Weak transcription	Aorta	Aorta
23	chr9:27148400-27148600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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