Variant report

Variant	rs3757150
Chromosome Location	chr6:26476782-26476783
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:9)
LncRNA
region (count:3)
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	chr6:26474445..26476878-chr6:26512542..26515226,3	K562	blood:
2	chr6:26462025..26466474-chr6:26476591..26479281,4	K562	blood:
3	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
4	chr6:26474221..26477564-chr6:26521186..26523081,3	K562	blood:
5	chr6:26476693..26479520-chr6:26480371..26483331,3	MCF-7	breast:
6	chr6:26470620..26472220-chr6:26474706..26477657,2	MCF-7	breast:
7	chr6:26462941..26465022-chr6:26475685..26477185,2	K562	blood:
8	chr6:26474090..26476155-chr6:26476306..26478036,2	MCF-7	breast:
9	chr6:26472961..26477109-chr6:26519664..26522390,3	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTN2A1-1	chr6:26476389-26476884	XLOC_005210
2	lnc-BTN2A1-1	chr6:26476545-26477465	XLOC_005210
3	lnc-ZNF322-2	chr6:26476380-26477377	NONHSAT147385

No data

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000199289	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10484443	1.00[CHB][hapmap]
rs12173854	0.81[CEU][hapmap]
rs12174602	0.81[CEU][hapmap]
rs12176129	0.85[ASN][1000 genomes]
rs12176317	0.85[CEU][hapmap]
rs13195047	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13210025	0.88[JPT][hapmap]
rs13214027	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13216828	0.81[CEU][hapmap]
rs16891717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891725	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16891790	1.00[CHB][hapmap]
rs16901784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1977	0.85[CEU][hapmap]
rs1978	0.85[CEU][hapmap]
rs2072803	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs2072806	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs2073529	0.85[CEU][hapmap]
rs2076030	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2093169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295593	0.85[ASN][1000 genomes]
rs2393657	0.86[ASN][1000 genomes]
rs2393665	0.86[ASN][1000 genomes]
rs2393667	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs34313099	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799380	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3799383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs3999471	0.92[JPT][hapmap]
rs4518487	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4634439	0.92[JPT][hapmap]
rs56296968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456727	0.91[EUR][1000 genomes]
rs6456728	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs67234939	0.85[ASN][1000 genomes]
rs6900118	0.89[CHB][hapmap]
rs6900665	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6911765	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6920256	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6924727	0.86[EUR][1000 genomes]
rs6926677	0.87[EUR][1000 genomes]
rs6933213	0.86[EUR][1000 genomes]
rs6941920	0.86[EUR][1000 genomes]
rs7740197	0.92[JPT][hapmap]
rs7756567	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759969	0.85[JPT][hapmap]
rs7773938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295702	0.93[JPT][hapmap]
rs9348712	0.81[CEU][hapmap]
rs9348716	0.81[CEU][hapmap]
rs9348718	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9348719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348720	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348721	0.94[ASN][1000 genomes]
rs9357007	0.86[ASN][1000 genomes]
rs9358932	0.85[CEU][hapmap]
rs9358934	0.81[CEU][hapmap]
rs9358935	0.81[CEU][hapmap]
rs9358937	0.81[CEU][hapmap]
rs9358938	0.89[CHB][hapmap]
rs9358944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358947	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358948	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366653	0.85[CEU][hapmap]
rs9366656	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs9366658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379851	0.85[CEU][hapmap]
rs9379855	0.85[CEU][hapmap]
rs9379856	0.85[CEU][hapmap]
rs9379857	0.81[CEU][hapmap]
rs9379858	0.85[CEU][hapmap]
rs9379859	0.85[CEU][hapmap]
rs9379864	0.81[CEU][hapmap]
rs9379875	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs9379877	0.87[ASN][1000 genomes]
rs9379880	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379882	0.85[ASN][1000 genomes]
rs9379893	0.92[JPT][hapmap]
rs9379895	0.92[JPT][hapmap]
rs9379897	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9379899	0.92[JPT][hapmap]
rs9379907	0.92[JPT][hapmap]
rs9393705	0.85[CEU][hapmap]
rs9393706	0.81[CEU][hapmap]
rs9393707	0.81[CEU][hapmap]
rs9393708	0.85[CEU][hapmap]
rs9393710	0.85[CEU][hapmap]
rs9393713	0.85[CEU][hapmap]
rs9393714	0.93[CEU][hapmap]
rs9393718	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs9393721	0.89[CHB][hapmap]
rs9393725	0.81[ASN][1000 genomes]
rs9393727	0.85[ASN][1000 genomes]
rs9393735	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9393737	0.92[JPT][hapmap]
rs9467772	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak 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	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3757150	BTN3A2	cis	Whole Blood	GTEx
rs3757150	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs3757150	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs3757150	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs3757150	BTN3A2	cis	lung	GTEx
rs3757150	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs3757150	BTN3A2	cis	Artery Tibial	GTEx
rs3757150	BTN3A2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26471800-26478000	Weak transcription	Lung	lung
2	chr6:26474600-26477000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:26475000-26476800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26475000-26476800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr6:26475000-26477000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:26475000-26477000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:26475000-26477200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:26475000-26477200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:26475200-26476800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:26475200-26476800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:26475200-26476800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:26475200-26476800	Enhancers	Small Intestine	intestine
13	chr6:26475200-26477000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:26475200-26477000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:26475200-26477000	Enhancers	Fetal Intestine Large	intestine
16	chr6:26475200-26481800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:26475400-26476800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:26475400-26476800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:26475400-26477000	Weak transcription	Fetal Stomach	stomach
20	chr6:26475400-26477200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:26475400-26478400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:26475400-26478400	Weak transcription	Colonic Mucosa	Colon
23	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:26475400-26479800	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:26475400-26480200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr6:26475600-26476800	Weak transcription	Liver	Liver
28	chr6:26475600-26476800	Weak transcription	Brain Angular Gyrus	brain
29	chr6:26475600-26477200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:26475600-26477200	Weak transcription	Right Atrium	heart
31	chr6:26475600-26477400	Weak transcription	Spleen	Spleen
32	chr6:26475600-26477600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:26475600-26477600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:26475600-26477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:26475600-26477800	Weak transcription	Fetal Heart	heart
36	chr6:26475600-26477800	Weak transcription	Placenta	Placenta
37	chr6:26475600-26478000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:26475600-26478200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:26475600-26479200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:26475600-26479200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:26475600-26479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:26475600-26481400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:26475800-26476800	Enhancers	Primary B cells from cord blood	blood
44	chr6:26475800-26476800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:26475800-26476800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:26475800-26477200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:26475800-26477200	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:26475800-26477200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr6:26475800-26477400	Weak transcription	Fetal Lung	lung
50	chr6:26475800-26477800	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links