Variant report

Variant	rs12698871
Chromosome Location	chr7:69674455-69674456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:12410651..12411212-chr7:69674323..69674880,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10234844	0.85[ASN][1000 genomes]
rs10235487	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10235781	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10235860	0.81[AMR][1000 genomes]
rs10237530	0.85[ASN][1000 genomes]
rs10237685	0.85[ASN][1000 genomes]
rs10251306	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10251416	0.85[ASN][1000 genomes]
rs10256186	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10257549	0.82[ASN][1000 genomes]
rs10258298	0.85[ASN][1000 genomes]
rs10258962	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10268235	0.90[ASN][1000 genomes]
rs10268924	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280622	0.85[ASN][1000 genomes]
rs1035010	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1035013	0.89[ASN][1000 genomes]
rs10452738	0.82[ASN][1000 genomes]
rs10486874	0.84[ASN][1000 genomes]
rs10486875	0.85[ASN][1000 genomes]
rs10499812	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11767997	0.93[ASN][1000 genomes]
rs11978431	0.82[ASN][1000 genomes]
rs12112638	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12155138	0.85[ASN][1000 genomes]
rs12374873	0.85[ASN][1000 genomes]
rs12698825	0.84[ASN][1000 genomes]
rs12698830	0.82[ASN][1000 genomes]
rs12698855	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698857	0.81[JPT][hapmap]
rs12698866	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12698877	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698895	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12698896	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs12698897	0.85[ASN][1000 genomes]
rs13221252	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13226538	0.82[ASN][1000 genomes]
rs13226923	0.85[ASN][1000 genomes]
rs13228123	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357759	0.83[CEU][hapmap]
rs1404274	0.84[ASN][1000 genomes]
rs1464787	0.86[ASN][1000 genomes]
rs1464788	0.86[ASN][1000 genomes]
rs1474368	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1524518	0.85[ASN][1000 genomes]
rs1880368	0.85[ASN][1000 genomes]
rs2280613	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2866277	0.85[ASN][1000 genomes]
rs28770244	0.82[ASN][1000 genomes]
rs35303761	0.85[ASN][1000 genomes]
rs3846984	0.85[ASN][1000 genomes]
rs6415223	0.90[ASN][1000 genomes]
rs6460536	0.96[ASN][1000 genomes]
rs6460537	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460541	0.85[ASN][1000 genomes]
rs6460542	0.85[ASN][1000 genomes]
rs6460543	0.85[ASN][1000 genomes]
rs6651055	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949651	0.92[ASN][1000 genomes]
rs6950485	0.93[ASN][1000 genomes]
rs6950647	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951921	0.82[ASN][1000 genomes]
rs6953170	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6954715	0.85[ASN][1000 genomes]
rs6954837	0.85[ASN][1000 genomes]
rs6961164	0.81[ASN][1000 genomes]
rs6961345	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962999	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6967986	0.82[ASN][1000 genomes]
rs6969375	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6975279	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976581	0.82[ASN][1000 genomes]
rs7781035	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7784584	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7788024	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7790729	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790934	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7791101	0.92[ASN][1000 genomes]
rs7792775	0.85[ASN][1000 genomes]
rs7792964	0.84[AMR][1000 genomes]
rs7794623	0.88[ASN][1000 genomes]
rs7795152	0.84[ASN][1000 genomes]
rs7796080	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797340	0.82[ASN][1000 genomes]
rs7798991	0.82[AMR][1000 genomes]
rs7805470	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7808540	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7809303	0.90[ASN][1000 genomes]
rs870920	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs873835	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	nsv607430	chr7:69658160-69702047	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12698871	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69655000-69692400	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69670200-69675600	Weak transcription	Psoas Muscle	Psoas
3	chr7:69670800-69674600	Enhancers	Fetal Intestine Small	intestine
4	chr7:69670800-69674800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:69671400-69676600	Weak transcription	Ovary	ovary
6	chr7:69672600-69674600	Enhancers	Fetal Intestine Large	intestine
7	chr7:69672600-69676000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:69673200-69676200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:69673400-69676200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:69673800-69675200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:69674000-69675600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:69674000-69678400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:69674200-69674600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:69674200-69675200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:69674200-69675600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:69674200-69678800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:69674400-69675800	Enhancers	Brain Germinal Matrix	brain

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