Variant report

Variant	rs4885350
Chromosome Location	chr13:76375317-76375318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:76375285-76375374	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

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[AFR][1000 genomes];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[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34348643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34713814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34782398	1.00[AFR][1000 genomes];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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843177	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]
rs4884020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885347	1.00[ASN][1000 genomes]
rs579540	0.86[ASN][1000 genomes]
rs71434807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71434809	1.00[AFR][1000 genomes];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
rs4885350	RAB12	trans	brain	seeQTL

Chromatin state (count:95 , 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	chr13:76361800-76377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:76362000-76376600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr13:76362600-76377000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:76363000-76377000	Weak transcription	GM12878-XiMat	blood
6	chr13:76363200-76376400	Weak transcription	Esophagus	oesophagus
7	chr13:76363200-76381800	Weak transcription	Fetal Stomach	stomach
8	chr13:76364600-76385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:76366400-76376600	Weak transcription	Left Ventricle	heart
10	chr13:76366400-76380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:76366800-76376600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:76366800-76379400	Weak transcription	Pancreas	Pancrea
13	chr13:76366800-76379400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:76366800-76380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:76366800-76380200	Weak transcription	Lung	lung
16	chr13:76367000-76377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:76367000-76379800	Weak transcription	Brain Angular Gyrus	brain
18	chr13:76367000-76380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:76367000-76387000	Weak transcription	Ovary	ovary
20	chr13:76367200-76377400	Weak transcription	Fetal Kidney	kidney
21	chr13:76367400-76377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:76367400-76380600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr13:76367400-76384400	Weak transcription	Fetal Lung	lung
24	chr13:76369600-76377400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr13:76369800-76376800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
27	chr13:76370800-76375800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:76370800-76378800	Genic enhancers	Osteobl	bone
29	chr13:76370800-76382400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr13:76371000-76375400	Genic enhancers	HSMM	muscle
31	chr13:76371400-76376600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:76371400-76376600	Weak transcription	Brain Anterior Caudate	brain
33	chr13:76371400-76379000	Weak transcription	Placenta	Placenta
34	chr13:76371600-76375400	Genic enhancers	NHLF	lung
35	chr13:76371600-76376400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:76371600-76377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr13:76371600-76377200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr13:76371800-76375600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr13:76371800-76376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:76371800-76377200	Enhancers	Fetal Heart	heart
41	chr13:76372000-76375600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:76372000-76376600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr13:76372000-76376600	Weak transcription	Fetal Thymus	thymus
44	chr13:76372000-76377200	Weak transcription	Small Intestine	intestine
45	chr13:76372000-76379600	Weak transcription	Colonic Mucosa	Colon
46	chr13:76372200-76376000	Weak transcription	Primary T cells from cord blood	blood
47	chr13:76372200-76376600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr13:76372200-76376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:76372200-76378400	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:76372400-76380200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links