Variant report

Variant	rs9837131
Chromosome Location	chr3:99854514-99854515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99847028..99850552-chr3:99852763..99855123,3	MCF-7	breast:
2	chr3:99835537..99838051-chr3:99853432..99855517,2	K562	blood:
3	chr3:99838255..99841576-chr3:99853652..99855888,3	K562	blood:
4	chr3:99839147..99841010-chr3:99854251..99856746,2	MCF-7	breast:
5	chr3:99847313..99849560-chr3:99852407..99855330,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10222474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12488245	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13059754	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs1387647	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2130369	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap]
rs35422475	0.81[EUR][1000 genomes]
rs4577503	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs4928150	0.92[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs4928151	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4928153	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4928237	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6440967	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6767441	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798114	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6802817	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6806323	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6808765	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs720688	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7619080	0.81[ASN][1000 genomes]
rs7629487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636776	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7649349	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs766778	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs902159	0.92[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs923472	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs9289981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811920	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849632	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865713	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9837131	EPHX1	trans	cerebellum	SCAN
rs9837131	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs9837131	SENP7	cis	parietal	SCAN
rs9837131	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:99843800-99855200	Weak transcription	Ovary	ovary
4	chr3:99845200-99855200	Weak transcription	Psoas Muscle	Psoas
5	chr3:99847000-99868800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:99849600-99855000	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:99850200-99861600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:99850600-99861400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:99850600-99861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:99854400-99855200	Weak transcription	Aorta	Aorta
11	chr3:99854400-99855200	Weak transcription	Right Atrium	heart

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