Variant report

Variant	rs4884020
Chromosome Location	chr13:76379297-76379298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10507834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100234	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap]
rs12859043	1.00[ASN][1000 genomes]
rs12871921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12872230	1.00[CEU][hapmap]
rs12877821	1.00[ASN][1000 genomes]
rs1323570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1470273	1.00[ASN][1000 genomes]
rs17065018	1.00[CHB][hapmap]
rs17065026	0.87[ASN][1000 genomes]
rs17065046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17065075	0.96[EUR][1000 genomes]
rs17065126	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17065132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34083520	1.00[ASN][1000 genomes]
rs34295825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34348643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34713814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34782398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35034793	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35353403	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4884019	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885347	1.00[ASN][1000 genomes]
rs4885350	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579540	0.86[ASN][1000 genomes]
rs71434807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71434809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920700	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4884020	RAB12	trans	brain	seeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:76363200-76381800	Weak transcription	Fetal Stomach	stomach
3	chr13:76364600-76385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:76366400-76380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76366800-76379400	Weak transcription	Pancreas	Pancrea
6	chr13:76366800-76379400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:76366800-76380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:76366800-76380200	Weak transcription	Lung	lung
9	chr13:76367000-76379800	Weak transcription	Brain Angular Gyrus	brain
10	chr13:76367000-76380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:76367000-76387000	Weak transcription	Ovary	ovary
12	chr13:76367400-76380600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:76367400-76384400	Weak transcription	Fetal Lung	lung
14	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
15	chr13:76370800-76382400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:76372000-76379600	Weak transcription	Colonic Mucosa	Colon
17	chr13:76372400-76380200	Weak transcription	Gastric	stomach
18	chr13:76373000-76414600	Weak transcription	HMEC	breast
19	chr13:76373200-76385800	Strong transcription	Hela-S3	cervix
20	chr13:76373400-76380800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:76373400-76387200	Weak transcription	Psoas Muscle	Psoas
22	chr13:76374400-76380200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:76374600-76380400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr13:76374800-76380600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr13:76374800-76382400	Strong transcription	Liver	Liver
26	chr13:76375000-76379400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr13:76375200-76383000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:76375400-76379600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr13:76375800-76382600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:76376200-76380800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr13:76376800-76380200	Weak transcription	Esophagus	oesophagus
32	chr13:76376800-76415400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:76377400-76379800	Genic enhancers	NHDF-Ad	bronchial
34	chr13:76377400-76380200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr13:76377400-76386800	Weak transcription	Stomach Mucosa	stomach
36	chr13:76377400-76395000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr13:76377600-76379600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr13:76377600-76380200	Weak transcription	Fetal Intestine Small	intestine
39	chr13:76377600-76380800	Strong transcription	Thymus	Thymus
40	chr13:76377600-76381000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr13:76377600-76381000	Weak transcription	Small Intestine	intestine
42	chr13:76377600-76382400	Strong transcription	NHLF	lung
43	chr13:76377600-76382600	Strong transcription	Fetal Intestine Large	intestine
44	chr13:76377600-76387000	Weak transcription	Brain Germinal Matrix	brain
45	chr13:76377600-76387200	Weak transcription	Spleen	Spleen
46	chr13:76377600-76395200	Weak transcription	GM12878-XiMat	blood
47	chr13:76377600-76398600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr13:76377600-76415800	Weak transcription	Dnd41	blood
49	chr13:76377600-76416200	Weak transcription	A549	lung
50	chr13:76377800-76380600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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