Variant report

Variant	rs12496392
Chromosome Location	chr3:20027837-20027838
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20027209..20028836-chr3:20081202..20083011,2	K562	blood:
2	chr3:20027598..20030041-chr3:20034679..20036338,2	K562	blood:
3	chr3:20027470..20029591-chr3:20033923..20036338,3	K562	blood:
4	chr3:20022682..20025378-chr3:20026127..20028940,2	MCF-7	breast:
5	chr3:20026744..20028391-chr3:20179736..20182279,2	MCF-7	breast:
6	chr3:20026329..20028709-chr3:20079789..20082702,2	K562	blood:
7	chr3:19997450..19999508-chr3:20025460..20027848,2	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11716116	0.92[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12486406	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496946	0.83[ASN][1000 genomes]
rs13078869	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13079277	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098043	0.82[ASN][1000 genomes]
rs13098054	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170342	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2623078	0.83[CHB][hapmap]
rs2686325	0.85[CEU][hapmap]
rs2929412	0.81[ASN][1000 genomes]
rs2948104	0.84[CHB][hapmap]
rs2948113	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34050713	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34468236	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34955379	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35094497	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35172759	0.83[ASN][1000 genomes]
rs35757621	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4302401	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858660	0.84[ASN][1000 genomes]
rs6778866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781143	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7625149	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968122	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12496392	RAB5A	cis	brain	BrainEAC
rs12496392	RAB5A	cis	cerebellar cortex	BrainEAC

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
2	chr3:20011800-20028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
4	chr3:20015200-20030000	Strong transcription	Fetal Thymus	thymus
5	chr3:20015400-20028200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:20015400-20028200	Strong transcription	Placenta	Placenta
7	chr3:20016200-20028000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:20021400-20028200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:20021800-20029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:20023000-20045800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:20023400-20029000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:20024000-20031200	Weak transcription	HSMM	muscle
13	chr3:20024000-20041400	Weak transcription	Ovary	ovary
14	chr3:20024200-20028600	Weak transcription	Colonic Mucosa	Colon
15	chr3:20024200-20030600	Weak transcription	Hela-S3	cervix
16	chr3:20024200-20031000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:20024200-20031200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:20024200-20031800	Weak transcription	Left Ventricle	heart
19	chr3:20024200-20033200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:20024200-20033400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:20024200-20036800	Weak transcription	Aorta	Aorta
22	chr3:20024200-20051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:20024400-20028600	Weak transcription	Brain Substantia Nigra	brain
24	chr3:20024400-20029000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:20024400-20029200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:20024400-20029800	Weak transcription	Spleen	Spleen
27	chr3:20024400-20030600	Weak transcription	Thymus	Thymus
28	chr3:20024400-20034000	Weak transcription	Brain Germinal Matrix	brain
29	chr3:20024600-20029000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:20024800-20029000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:20024800-20030800	Weak transcription	Fetal Stomach	stomach
32	chr3:20024800-20031600	Weak transcription	Lung	lung
33	chr3:20024800-20031800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:20025000-20028400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:20025200-20028400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:20025400-20028600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:20025400-20028600	Weak transcription	GM12878-XiMat	blood
38	chr3:20025400-20029000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:20025400-20029000	Weak transcription	NHDF-Ad	bronchial
40	chr3:20025400-20029600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:20025400-20030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:20025400-20031800	Weak transcription	Fetal Brain Female	brain
43	chr3:20025400-20033200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:20025600-20028400	Weak transcription	Fetal Lung	lung
45	chr3:20025600-20028600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:20025600-20028600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:20025600-20029000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:20025600-20029000	Weak transcription	K562	blood
49	chr3:20025600-20033400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:20025800-20028400	Weak transcription	Primary hematopoietic stem cells	blood

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