Variant report

Variant	rs9295702
Chromosome Location	chr6:26634040-26634041
allele	C/T
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	chr6:26633557-26634290	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-5	chr6:26630055-26634786	NONHSAT108301

Variant related genes	Relation type
VN1R14P	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11967852	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13195210	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208916	0.83[ASN][1000 genomes]
rs13210025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214027	0.93[JPT][hapmap]
rs13215020	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16891725	0.92[JPT][hapmap]
rs16891790	1.00[CHB][hapmap]
rs16901784	0.92[JPT][hapmap]
rs2093169	0.92[JPT][hapmap]
rs28360517	0.83[ASN][1000 genomes]
rs3734544	0.92[JPT][hapmap]
rs3757150	0.93[JPT][hapmap]
rs3799383	0.92[JPT][hapmap]
rs3999471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4634439	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6920256	0.92[JPT][hapmap]
rs6936555	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936561	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740197	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759969	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773938	0.92[JPT][hapmap]
rs9348726	0.83[ASN][1000 genomes]
rs9348727	0.86[CHB][hapmap]
rs9348728	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358944	0.92[JPT][hapmap]
rs9358945	0.92[JPT][hapmap]
rs9358946	0.92[JPT][hapmap]
rs9366658	0.92[JPT][hapmap]
rs9368443	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368445	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368447	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368448	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368450	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9368451	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379897	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9379899	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9379901	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9379905	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393735	0.93[JPT][hapmap]
rs9393737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393739	0.95[AMR][1000 genomes];0.98[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9295702	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9295702	BTN3A2	cis	Whole Blood	GTEx
rs9295702	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9295702	BTN3A2	cis	lung	GTEx
rs9295702	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9295702	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26625400-26639200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:26629400-26639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:26629600-26635400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:26629800-26640000	Weak transcription	Left Ventricle	heart
5	chr6:26630400-26640000	Weak transcription	Aorta	Aorta
6	chr6:26631400-26634600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:26631400-26639000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:26631800-26634200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:26631800-26634400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:26631800-26634800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:26631800-26639200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:26631800-26640400	Weak transcription	Pancreas	Pancrea
13	chr6:26632000-26640600	Weak transcription	Fetal Stomach	stomach
14	chr6:26632200-26639000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:26632200-26639200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:26632200-26639200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:26632400-26634600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:26632400-26639000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:26632600-26638200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:26632600-26638800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:26632600-26638800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:26632600-26639000	Weak transcription	Dnd41	blood
23	chr6:26632600-26640000	Weak transcription	Fetal Kidney	kidney
24	chr6:26632800-26634400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:26632800-26634600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:26632800-26638400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:26632800-26639000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:26632800-26639200	Weak transcription	Psoas Muscle	Psoas
29	chr6:26632800-26640000	Weak transcription	Esophagus	oesophagus
30	chr6:26633000-26634400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:26633000-26639000	Weak transcription	HepG2	liver
32	chr6:26633000-26639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:26633000-26639200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:26633000-26639200	Weak transcription	Right Ventricle	heart
35	chr6:26633000-26639400	Weak transcription	Colonic Mucosa	Colon
36	chr6:26633000-26640400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:26633000-26658000	Weak transcription	Fetal Brain Male	brain
38	chr6:26633200-26634200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:26633200-26638200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:26633200-26639800	Weak transcription	Gastric	stomach
41	chr6:26633200-26640000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:26633400-26634600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:26633400-26634600	ZNF genes & repeats	HSMM	muscle
44	chr6:26633400-26639000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:26633400-26639200	Weak transcription	Primary T cells from cord blood	blood
46	chr6:26633400-26639200	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:26633400-26640000	Weak transcription	Spleen	Spleen
48	chr6:26633400-26640600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:26633600-26634600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
50	chr6:26633600-26634600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links