Variant report

Variant	rs9379899
Chromosome Location	chr6:26603015-26603016
allele	A/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26602321..26604029-chr6:26608218..26609834,2	MCF-7	breast:
2	chr6:26602899..26604701-chr6:27090642..27092939,2	MCF-7	breast:
3	chr6:26345126..26347534-chr6:26601972..26604774,2	K562	blood:
4	chr6:26602910..26606507-chr6:26613473..26615906,4	K562	blood:
5	chr6:26601646..26604594-chr6:26657057..26659318,2	K562	blood:
6	chr6:26601738..26604089-chr6:26631251..26632844,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-1	chr6:26602961-26603819	XLOC_005213

No data

Variant related genes	Relation type
ENSG00000218346	Chromatin interaction
ENSG00000272468	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11967852	0.86[ASN][1000 genomes]
rs12176129	0.83[AMR][1000 genomes]
rs13195210	0.83[ASN][1000 genomes]
rs13195509	0.85[CEU][hapmap]
rs13208916	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13214027	0.92[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs13215020	0.80[ASN][1000 genomes]
rs13220261	0.83[CEU][hapmap]
rs16891725	0.92[JPT][hapmap]
rs16891790	1.00[CHB][hapmap]
rs16901784	0.93[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes]
rs2093169	0.92[JPT][hapmap]
rs28360517	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734542	0.84[CEU][hapmap]
rs3734544	0.92[JPT][hapmap]
rs3757150	0.92[JPT][hapmap]
rs3799383	0.93[CEU][hapmap];0.92[JPT][hapmap]
rs3823158	0.86[CEU][hapmap]
rs3999471	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4634439	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67234939	0.89[AMR][1000 genomes]
rs6920256	0.93[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes]
rs6936555	0.83[ASN][1000 genomes]
rs6936561	0.83[ASN][1000 genomes]
rs7740197	1.00[JPT][hapmap]
rs7759969	0.92[JPT][hapmap]
rs7773938	0.92[JPT][hapmap]
rs9295702	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9348726	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348727	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9348728	0.83[ASN][1000 genomes]
rs9358944	0.92[JPT][hapmap]
rs9358945	0.92[JPT][hapmap]
rs9358946	0.92[JPT][hapmap]
rs9366658	0.92[JPT][hapmap]
rs9368442	0.88[ASN][1000 genomes]
rs9368443	0.89[ASN][1000 genomes]
rs9368445	0.83[ASN][1000 genomes]
rs9368447	0.83[ASN][1000 genomes]
rs9368448	0.83[ASN][1000 genomes]
rs9368450	0.80[ASN][1000 genomes]
rs9368451	0.80[ASN][1000 genomes]
rs9379891	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9379893	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379895	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379901	1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379905	0.83[ASN][1000 genomes]
rs9379907	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9393735	0.93[CEU][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs9393737	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9393739	0.83[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9379899	BTN3A2	cis	uninvolved skin	skin_eQTL
rs9379899	BTN3A2	cis	Artery Aorta	GTEx
rs9379899	BTN3A2	cis	Thyroid	GTEx
rs9379899	BTN3A2	cis	Whole Blood	GTEx
rs9379899	BTN3A2	cis	Nerve Tibial	GTEx
rs9379899	BTN3A2	cis	Artery Tibial	GTEx
rs9379899	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs9379899	BTN3A2	cis	multi-tissue	Pritchard
rs9379899	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9379899	BTN3A2	cis	lung	GTEx
rs9379899	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9379899	BTN3A2	cis	normal skin	skin_eQTL
rs9379899	BTN3A2	cis	Muscle Skeletal	GTEx
rs9379899	BTN3A2	cis	Heart Left Ventricle	GTEx
rs9379899	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9379899	BTN3A2	cis	Esophagus Mucosa	GTEx
rs9379899	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26598000-26604800	Weak transcription	Aorta	Aorta
2	chr6:26598000-26606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:26598200-26607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:26598600-26603200	Weak transcription	Fetal Brain Male	brain
5	chr6:26599200-26607800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:26599200-26607800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:26599200-26607800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:26599400-26607800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:26599600-26603200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:26599600-26607800	Weak transcription	Colonic Mucosa	Colon
11	chr6:26599800-26607800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:26600000-26603800	Weak transcription	Gastric	stomach
13	chr6:26600000-26604400	Weak transcription	HUVEC	blood vessel
14	chr6:26600000-26607800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:26600000-26607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:26600000-26607800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:26600000-26607800	Weak transcription	Fetal Stomach	stomach
18	chr6:26600000-26607800	Weak transcription	Thymus	Thymus
19	chr6:26600000-26607800	Weak transcription	HepG2	liver
20	chr6:26600000-26607800	Weak transcription	NHLF	lung
21	chr6:26600000-26614000	Weak transcription	Spleen	Spleen
22	chr6:26600200-26603400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:26600200-26603600	Weak transcription	NH-A	brain
24	chr6:26600200-26603800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:26600200-26603800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:26600200-26604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:26600200-26607200	Weak transcription	Brain Germinal Matrix	brain
28	chr6:26600200-26607600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:26600200-26607600	Weak transcription	Hela-S3	cervix
30	chr6:26600200-26607800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr6:26600200-26607800	Weak transcription	Brain Angular Gyrus	brain
32	chr6:26600200-26607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:26600200-26607800	Weak transcription	Fetal Kidney	kidney
34	chr6:26600200-26607800	Weak transcription	Dnd41	blood
35	chr6:26600200-26607800	Weak transcription	HMEC	breast
36	chr6:26600200-26607800	Weak transcription	Osteobl	bone
37	chr6:26600400-26603200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:26600400-26603800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:26600400-26603800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:26600400-26607800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:26600400-26607800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:26600400-26607800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:26600400-26607800	Weak transcription	Liver	Liver
44	chr6:26600400-26607800	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:26600400-26607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:26600400-26607800	Weak transcription	Ovary	ovary
47	chr6:26600400-26607800	Weak transcription	A549	lung
48	chr6:26600400-26607800	Weak transcription	NHDF-Ad	bronchial
49	chr6:26600600-26605800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:26600600-26607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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