Variant report

Variant	rs12698855
Chromosome Location	chr7:69596963-69596964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10234614	0.83[EUR][1000 genomes]
rs10234844	0.82[ASN][1000 genomes]
rs10234892	0.82[EUR][1000 genomes]
rs10235487	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235781	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10235860	0.82[AMR][1000 genomes]
rs10237530	0.82[ASN][1000 genomes]
rs10237685	0.82[ASN][1000 genomes]
rs10251306	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10251416	0.82[ASN][1000 genomes]
rs10256186	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10257549	0.85[ASN][1000 genomes]
rs10258298	0.81[ASN][1000 genomes]
rs10258962	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10268235	0.94[ASN][1000 genomes]
rs10268924	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10279392	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10280622	0.82[ASN][1000 genomes]
rs1035010	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035013	0.92[ASN][1000 genomes]
rs10452738	0.85[ASN][1000 genomes]
rs10486874	0.81[ASN][1000 genomes]
rs10486875	0.82[ASN][1000 genomes]
rs10499812	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10950199	0.83[EUR][1000 genomes]
rs11508453	0.81[ASN][1000 genomes]
rs11767997	0.96[ASN][1000 genomes]
rs11978431	0.85[ASN][1000 genomes]
rs12112638	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12155138	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12374873	0.81[ASN][1000 genomes]
rs12698816	0.81[ASN][1000 genomes]
rs12698825	0.87[ASN][1000 genomes]
rs12698830	0.85[ASN][1000 genomes]
rs12698842	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12698849	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12698857	0.81[JPT][hapmap]
rs12698866	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12698871	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698877	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698895	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12698896	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12698897	0.81[ASN][1000 genomes]
rs13221252	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13226538	0.85[ASN][1000 genomes]
rs13226923	0.82[ASN][1000 genomes]
rs13228123	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237811	0.83[ASN][1000 genomes]
rs1357759	0.88[CEU][hapmap]
rs1404274	0.81[ASN][1000 genomes]
rs1464787	0.83[ASN][1000 genomes]
rs1464788	0.83[ASN][1000 genomes]
rs1474368	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1524518	0.82[ASN][1000 genomes]
rs1880368	0.81[ASN][1000 genomes]
rs2222544	0.82[EUR][1000 genomes]
rs2280613	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2866277	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28770244	0.85[ASN][1000 genomes]
rs35303761	0.82[ASN][1000 genomes]
rs35696945	0.83[ASN][1000 genomes]
rs3846984	0.81[ASN][1000 genomes]
rs6415223	0.93[ASN][1000 genomes]
rs6460536	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6460537	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460541	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460542	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460543	0.81[ASN][1000 genomes]
rs6651055	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949651	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6950485	0.96[ASN][1000 genomes]
rs6950647	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951921	0.85[ASN][1000 genomes]
rs6953170	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6954715	0.81[ASN][1000 genomes]
rs6954837	0.81[ASN][1000 genomes]
rs6961164	0.85[ASN][1000 genomes]
rs6961345	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6962999	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6969375	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6975279	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976581	0.81[EUR][1000 genomes]
rs6979355	0.81[ASN][1000 genomes]
rs7781035	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7781401	0.81[EUR][1000 genomes]
rs7781727	0.81[EUR][1000 genomes]
rs7784584	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7787612	0.82[EUR][1000 genomes]
rs7788024	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7790729	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790934	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7791101	0.96[ASN][1000 genomes]
rs7792775	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7792964	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7794623	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7795152	0.87[ASN][1000 genomes]
rs7796080	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7796973	0.81[ASN][1000 genomes]
rs7797340	0.85[ASN][1000 genomes]
rs7798991	0.82[EUR][1000 genomes]
rs7799308	0.82[EUR][1000 genomes]
rs7805470	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7808540	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7809303	0.93[ASN][1000 genomes]
rs7809934	0.85[ASN][1000 genomes]
rs8180850	0.83[EUR][1000 genomes]
rs870920	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs873835	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877687	0.81[ASN][1000 genomes]
rs9638268	0.92[AMR][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	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018289	chr7:69383450-69650885	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538922	chr7:69383450-69650885	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1020488	chr7:69465268-69671126	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12698855	VKORC1L1	cis	parietal	SCAN
rs12698855	WBSCR17	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69582000-69597600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:69586200-69597800	Weak transcription	Left Ventricle	heart
3	chr7:69587000-69599400	Weak transcription	Primary B cells from cord blood	blood
4	chr7:69590200-69597000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:69591600-69602400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr7:69593200-69599200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:69593400-69597600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:69594600-69600000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:69595000-69597400	Enhancers	Fetal Brain Male	brain
10	chr7:69595200-69599800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:69595400-69597600	Enhancers	Brain Germinal Matrix	brain
12	chr7:69595400-69599800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:69595600-69597800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:69595800-69597000	Weak transcription	Fetal Brain Female	brain
15	chr7:69596000-69597200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:69596000-69597200	Weak transcription	HSMMtube	muscle
17	chr7:69596600-69600200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:69596800-69598600	Enhancers	HSMM	muscle
19	chr7:69596800-69599400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:69596800-69599400	Enhancers	Fetal Muscle Leg	muscle
21	chr7:69596800-69599800	Enhancers	Fetal Stomach	stomach
22	chr7:69596800-69602200	Enhancers	Fetal Heart	heart

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