Variant report

Variant	rs793469
Chromosome Location	chr3:99537305-99537306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99536894..99538407-chr3:99549555..99551120,2	K562	blood:
2	chr3:99534888..99538188-chr3:99978029..99981295,5	K562	blood:
3	chr11:62609023..62609533-chr3:99536736..99537348,2	Hela-S3	cervix:
4	chr3:99535897..99537944-chr3:99594142..99596963,2	K562	blood:
5	chr3:99534048..99538188-chr3:99977608..99981959,7	K562	blood:
6	chr3:99534190..99537845-chr3:99978822..99982000,3	MCF-7	breast:
7	chr3:99535720..99537944-chr3:99593016..99595642,2	K562	blood:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000036054	Chromatin interaction
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10936003	0.80[AFR][1000 genomes]
rs16841874	0.90[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap]
rs1718235	0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs1718240	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2449106	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4244712	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4928230	0.88[LWK][hapmap];0.90[MKK][hapmap]
rs6805884	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs704572	0.81[YRI][hapmap]
rs7650727	0.82[LWK][hapmap];0.88[MKK][hapmap]
rs793439	0.88[LWK][hapmap];0.90[MKK][hapmap]
rs793450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs793482	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs793498	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793502	0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs813218	0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs793469	EPHX1	trans	cerebellum	SCAN
rs793469	SENP7	cis	parietal	SCAN
rs793469	OR5H6	cis	cerebellum	SCAN
rs793469	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99535600-99537400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:99535600-99537400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:99535600-99537400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:99535600-99537400	Active TSS	Thymus	Thymus
5	chr3:99535600-99537400	Active TSS	A549	lung
6	chr3:99535600-99537600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:99535600-99537600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:99535600-99537600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:99535600-99537800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:99535600-99537800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:99535600-99538000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:99535600-99538000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:99535600-99538000	Active TSS	Psoas Muscle	Psoas
14	chr3:99535800-99537400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:99535800-99537400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:99535800-99537400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:99535800-99537400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:99535800-99537400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:99535800-99537400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:99535800-99537400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:99535800-99537400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:99535800-99537400	Active TSS	Fetal Brain Male	brain
23	chr3:99535800-99537400	Active TSS	Fetal Muscle Trunk	muscle
24	chr3:99535800-99537400	Active TSS	Left Ventricle	heart
25	chr3:99535800-99537400	Active TSS	Ovary	ovary
26	chr3:99535800-99537400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr3:99535800-99537600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:99535800-99537600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:99535800-99537600	Active TSS	Fetal Muscle Leg	muscle
30	chr3:99535800-99537600	Active TSS	Fetal Stomach	stomach
31	chr3:99535800-99537600	Active TSS	Pancreas	Pancrea
32	chr3:99535800-99537600	Active TSS	Right Atrium	heart
33	chr3:99535800-99537600	Active TSS	Right Ventricle	heart
34	chr3:99535800-99538000	Active TSS	K562	blood
35	chr3:99536000-99537400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr3:99536000-99537400	Active TSS	Aorta	Aorta
37	chr3:99536000-99537400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:99536000-99537400	Active TSS	Gastric	stomach
39	chr3:99536000-99537600	Active TSS	NHDF-Ad	bronchial
40	chr3:99536000-99537800	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:99536000-99537800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:99536200-99537400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:99536200-99537400	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr3:99536200-99537400	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:99536200-99537400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:99536200-99537400	Active TSS	Fetal Intestine Small	intestine
47	chr3:99536200-99537400	Active TSS	Placenta	Placenta
48	chr3:99536200-99537400	Active TSS	Stomach Smooth Muscle	stomach
49	chr3:99536200-99537400	Active TSS	NHEK	skin
50	chr3:99536200-99537400	Active TSS	NHLF	lung

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