Variant report

Variant	rs13200462
Chromosome Location	chr6:28218199-28218200
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28129539..28132293-chr6:28218155..28220468,2	K562	blood:
2	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
3	chr6:28107426..28110018-chr6:28217244..28218841,2	MCF-7	breast:
4	chr6:28217257..28219975-chr6:28319678..28321725,2	K562	blood:
5	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
6	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
7	chr6:28104411..28106188-chr6:28216933..28220029,3	MCF-7	breast:
8	chr6:28217084..28219662-chr6:28271676..28274035,2	K562	blood:
9	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10456362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076639	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11755032	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11965538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12000	0.80[YRI][hapmap]
rs1321505	0.93[CEU][hapmap]
rs1339899	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1419183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778507	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1778508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936365	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213239	1.00[JPT][hapmap]
rs213241	1.00[JPT][hapmap]
rs213243	1.00[JPT][hapmap]
rs213244	1.00[JPT][hapmap]
rs2743554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2743555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757188	0.93[CEU][hapmap]
rs4713139	0.93[CEU][hapmap]
rs4713140	0.93[CEU][hapmap]
rs61127718	0.80[ASN][1000 genomes]
rs68141011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6905391	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920512	0.83[CHB][hapmap];0.91[ASN][1000 genomes]
rs735765	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7740487	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853676	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853679	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853681	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853685	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853687	0.81[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295765	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9380064	0.93[CEU][hapmap]
rs9380069	0.93[CEU][hapmap]
rs9393908	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs9461443	0.81[YRI][hapmap]
rs9461446	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461448	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9461449	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9468287	0.93[CEU][hapmap]
rs9468318	0.81[CEU][hapmap]
rs9468321	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468322	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468342	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9468345	1.00[JPT][hapmap]
rs9986596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13200462	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13200462	AL022393.7	cis	Muscle Skeletal	GTEx
rs13200462	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13200462	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13200462	RP5-874C20.3	cis	Thyroid	GTEx
rs13200462	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs13200462	RP5-874C20.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
3	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:28203000-28218400	Weak transcription	HUVEC	blood vessel
5	chr6:28212800-28218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:28213600-28218400	Weak transcription	Fetal Heart	heart
7	chr6:28213600-28218400	Weak transcription	NHEK	skin
8	chr6:28213800-28218200	Weak transcription	HMEC	breast
9	chr6:28214000-28218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:28214200-28218400	Weak transcription	Small Intestine	intestine
11	chr6:28214200-28218400	Weak transcription	Hela-S3	cervix
12	chr6:28214400-28218400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:28214400-28219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28214600-28218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:28214600-28219200	Weak transcription	Gastric	stomach
16	chr6:28214600-28219400	Weak transcription	Aorta	Aorta
17	chr6:28214800-28218400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:28214800-28218400	Weak transcription	Spleen	Spleen
19	chr6:28214800-28218400	Weak transcription	A549	lung
20	chr6:28214800-28218400	Weak transcription	NHDF-Ad	bronchial
21	chr6:28215000-28218200	Weak transcription	Fetal Kidney	kidney
22	chr6:28215000-28218400	Weak transcription	HSMM	muscle
23	chr6:28215000-28218400	Weak transcription	Osteobl	bone
24	chr6:28215000-28218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:28215000-28218600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28215000-28218600	Weak transcription	Colonic Mucosa	Colon
27	chr6:28215000-28218600	Weak transcription	Right Ventricle	heart
28	chr6:28215200-28218400	Weak transcription	K562	blood
29	chr6:28215400-28218400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:28215600-28218400	Weak transcription	Brain Angular Gyrus	brain
31	chr6:28215600-28218400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:28215600-28218400	Weak transcription	NH-A	brain
33	chr6:28215800-28218200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:28215800-28218600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:28216000-28218400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:28216000-28218400	Weak transcription	Fetal Brain Female	brain
37	chr6:28216000-28219200	Weak transcription	Lung	lung
38	chr6:28216200-28218200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:28216200-28218200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:28216200-28218200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:28216200-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:28216200-28218400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:28216200-28218400	Weak transcription	Brain Anterior Caudate	brain
44	chr6:28216200-28218400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:28216200-28218400	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:28216200-28218400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:28216200-28218400	Weak transcription	Ovary	ovary
48	chr6:28216200-28218600	Weak transcription	HSMMtube	muscle
49	chr6:28216200-28219400	Weak transcription	Esophagus	oesophagus
50	chr6:28216400-28218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links