Variant report

Variant	rs513349
Chromosome Location	chr6:33541719-33541720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs210134	0.83[LWK][hapmap];0.87[YRI][hapmap]
rs210139	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs210140	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs210141	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs210145	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs210146	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210148	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs549888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv519079	chr6:33540209-33542538	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	23263863	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs513349	BAK1	cis	Whole Blood	GTEx
rs513349	BAK1	Cis_1M	lymphoblastoid	RTeQTL
rs513349	BAK1	cis	Muscle Skeletal	GTEx
rs513349	BAK1	cis	lymphoblastoid	seeQTL
rs513349	BAK1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33539200-33547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33539400-33541800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:33539600-33541800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:33539600-33541800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:33539600-33541800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:33539600-33541800	Weak transcription	Small Intestine	intestine
7	chr6:33539600-33542000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:33539600-33542000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:33539600-33542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:33539600-33542000	Weak transcription	HUVEC	blood vessel
11	chr6:33539600-33542800	Weak transcription	A549	lung
12	chr6:33539600-33546200	Weak transcription	NHDF-Ad	bronchial
13	chr6:33539600-33546400	Weak transcription	Fetal Brain Male	brain
14	chr6:33539600-33547000	Weak transcription	Fetal Kidney	kidney
15	chr6:33539800-33541800	Weak transcription	Liver	Liver
16	chr6:33539800-33541800	Weak transcription	Esophagus	oesophagus
17	chr6:33539800-33541800	Weak transcription	Fetal Lung	lung
18	chr6:33539800-33542000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:33539800-33542000	Weak transcription	HepG2	liver
20	chr6:33539800-33542000	Weak transcription	HSMMtube	muscle
21	chr6:33539800-33542000	Weak transcription	NH-A	brain
22	chr6:33539800-33542200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:33539800-33542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:33539800-33544400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:33539800-33544400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:33539800-33545400	Strong transcription	Fetal Intestine Small	intestine
27	chr6:33539800-33546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:33539800-33547000	Weak transcription	Psoas Muscle	Psoas
29	chr6:33540000-33541800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:33540000-33541800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:33540000-33541800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:33540000-33542000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:33540000-33542000	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:33540000-33542200	Weak transcription	Stomach Mucosa	stomach
35	chr6:33540000-33543800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr6:33540000-33544200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:33540000-33545000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:33540000-33545000	Weak transcription	Right Atrium	heart
39	chr6:33540000-33546400	Strong transcription	Fetal Stomach	stomach
40	chr6:33540200-33541800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:33540200-33541800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:33540200-33541800	Weak transcription	Brain Anterior Caudate	brain
43	chr6:33540200-33541800	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:33540200-33541800	Weak transcription	Right Ventricle	heart
45	chr6:33540200-33541800	Weak transcription	K562	blood
46	chr6:33540200-33542200	Weak transcription	Primary B cells from cord blood	blood
47	chr6:33540200-33542200	Weak transcription	Hela-S3	cervix
48	chr6:33540200-33543200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:33540200-33543600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:33540200-33544800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links