Variant report

Variant	rs1407045
Chromosome Location	chr6:26476155-26476156
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26474445..26476878-chr6:26512542..26515226,3	K562	blood:
2	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
3	chr6:26474221..26477564-chr6:26521186..26523081,3	K562	blood:
4	chr6:26314124..26316500-chr6:26474166..26476547,2	K562	blood:
5	chr6:26474337..26476257-chr6:26519630..26521866,2	MCF-7	breast:
6	chr6:26156628..26158808-chr6:26474596..26476734,2	MCF-7	breast:
7	chr6:26470620..26472220-chr6:26474706..26477657,2	MCF-7	breast:
8	chr6:26462941..26465022-chr6:26475685..26477185,2	K562	blood:
9	chr6:26474090..26476155-chr6:26476306..26478036,2	MCF-7	breast:
10	chr6:26472961..26477109-chr6:26519664..26522390,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228223	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1056668	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12525684	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12526680	0.83[CEU][hapmap]
rs1321479	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1321481	0.80[CHB][hapmap]
rs1614887	0.85[CEU][hapmap];0.93[LWK][hapmap]
rs1624440	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1796520	0.90[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1796521	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes]
rs1796522	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1884947	0.81[TSI][hapmap]
rs1977198	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2024970	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2145318	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2208331	0.81[EUR][1000 genomes]
rs2255070	0.82[EUR][1000 genomes]
rs35355150	0.82[EUR][1000 genomes]
rs3734540	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736781	0.82[EUR][1000 genomes]
rs3736782	0.82[EUR][1000 genomes]
rs4573	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs4713008	0.81[CEU][hapmap]
rs6903973	0.82[EUR][1000 genomes]
rs6926629	0.82[EUR][1000 genomes]
rs71544291	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs742090	0.90[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7755997	0.86[ASN][1000 genomes]
rs7763910	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs9295689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9379887	0.80[EUR][1000 genomes]
rs9461259	0.82[EUR][1000 genomes]
rs9467774	0.82[CEU][hapmap];0.82[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1407045	BTN3A2	cis	cerebellum	SCAN
rs1407045	BTN3A3	cis	parietal	SCAN
rs1407045	HIST1H2BD	cis	lymphoblastoid	seeQTL
rs1407045	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs1407045	ZNF204P	cis	cerebellum	SCAN
rs1407045	BTN3A2	cis	parietal	SCAN
rs1407045	HCG11	cis	normal skin	skin_eQTL
rs1407045	BTN3A3	cis	cerebellum	SCAN
rs1407045	RP11-457M11.5	cis	Artery Tibial	GTEx
rs1407045	BTN3A1	cis	parietal	SCAN
rs1407045	DCDC2	cis	cerebellum	SCAN
rs1407045	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs1407045	BTN3A2	cis	lymphoblastoid	seeQTL
rs1407045	HIST1H3D	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26469600-26476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:26471800-26476400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:26471800-26478000	Weak transcription	Lung	lung
4	chr6:26473600-26476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:26474600-26477000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:26475000-26476200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:26475000-26476600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:26475000-26476600	Enhancers	Hela-S3	cervix
9	chr6:26475000-26476600	Enhancers	NH-A	brain
10	chr6:26475000-26476800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:26475000-26476800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:26475000-26477000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:26475000-26477000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:26475000-26477200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:26475000-26477200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:26475200-26476400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:26475200-26476400	Enhancers	Fetal Intestine Small	intestine
18	chr6:26475200-26476600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:26475200-26476600	Enhancers	Fetal Thymus	thymus
20	chr6:26475200-26476600	Enhancers	HUVEC	blood vessel
21	chr6:26475200-26476600	Enhancers	NHDF-Ad	bronchial
22	chr6:26475200-26476800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:26475200-26476800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:26475200-26476800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:26475200-26476800	Enhancers	Small Intestine	intestine
26	chr6:26475200-26477000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:26475200-26477000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:26475200-26477000	Enhancers	Fetal Intestine Large	intestine
29	chr6:26475200-26481800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:26475400-26476400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:26475400-26476800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:26475400-26476800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:26475400-26477000	Weak transcription	Fetal Stomach	stomach
34	chr6:26475400-26477200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:26475400-26478400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:26475400-26478400	Weak transcription	Colonic Mucosa	Colon
37	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:26475400-26479800	Enhancers	Primary B cells from peripheral blood	blood
40	chr6:26475400-26480200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:26475600-26476200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr6:26475600-26476400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:26475600-26476400	Weak transcription	Brain Germinal Matrix	brain
44	chr6:26475600-26476400	Weak transcription	Esophagus	oesophagus
45	chr6:26475600-26476600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:26475600-26476600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:26475600-26476600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:26475600-26476600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:26475600-26476600	Enhancers	Stomach Mucosa	stomach
50	chr6:26475600-26476600	Enhancers	NHLF	lung

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