Variant report

Variant	rs1078931
Chromosome Location	chr11:45203848-45203849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45164160..45171283-chr11:45198764..45207868,26	MCF-7	breast:
2	chr11:45167893..45171206-chr11:45200303..45204446,5	MCF-7	breast:
3	chr11:45167440..45169930-chr11:45202656..45204248,2	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1075293	0.91[GIH][hapmap]
rs10838430	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11038296	0.91[GIH][hapmap]
rs11038318	0.81[GIH][hapmap]
rs11038359	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12363331	0.95[EUR][1000 genomes]
rs12363718	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1487719	0.81[GIH][hapmap]
rs2077427	0.91[GIH][hapmap]
rs2863156	1.00[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2863159	0.89[TSI][hapmap]
rs2863160	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2863161	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs2863168	0.84[EUR][1000 genomes]
rs2863169	0.84[EUR][1000 genomes]
rs2863171	0.89[TSI][hapmap]
rs4531454	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4755309	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4755947	0.83[EUR][1000 genomes]
rs4755950	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6416127	0.85[TSI][hapmap]
rs7122974	0.84[GIH][hapmap]
rs7126559	0.83[EUR][1000 genomes]
rs73466442	0.84[EUR][1000 genomes]
rs7480089	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7943729	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	esv3326620	chr11:45201401-45203949	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1078931	OR4X2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45201800-45204000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:45202000-45204600	Weak transcription	Liver	Liver
3	chr11:45202000-45205400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:45202000-45206600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:45202000-45207600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:45202000-45220000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:45202200-45204600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:45202400-45204200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:45202600-45204000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:45202600-45204600	Weak transcription	Primary B cells from cord blood	blood
11	chr11:45202800-45204000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:45202800-45204000	Flanking Active TSS	Hela-S3	cervix
13	chr11:45202800-45206200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:45202800-45234000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:45203000-45204000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:45203000-45204000	Weak transcription	Fetal Brain Female	brain
17	chr11:45203000-45204000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
18	chr11:45203000-45204200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:45203000-45204200	Enhancers	Brain Substantia Nigra	brain
20	chr11:45203000-45204200	Enhancers	Gastric	stomach
21	chr11:45203000-45204400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:45203000-45204800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:45203000-45206400	Weak transcription	NHDF-Ad	bronchial
24	chr11:45203000-45208400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:45203000-45209600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:45203000-45213400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:45203000-45237000	Weak transcription	Small Intestine	intestine
28	chr11:45203200-45204000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:45203200-45204000	Enhancers	Ovary	ovary
30	chr11:45203200-45204200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr11:45203200-45204400	Enhancers	Colon Smooth Muscle	Colon
32	chr11:45203200-45204600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:45203200-45204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:45203200-45204800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:45203200-45204800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:45203200-45205000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:45203200-45205000	Weak transcription	HSMMtube	muscle
38	chr11:45203200-45205000	Weak transcription	K562	blood
39	chr11:45203200-45205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:45203200-45206200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:45203200-45208400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:45203200-45209600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:45203200-45211000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:45203200-45212400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:45203200-45213000	Weak transcription	HSMM	muscle
46	chr11:45203200-45215200	Weak transcription	Psoas Muscle	Psoas
47	chr11:45203400-45204000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:45203400-45204000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:45203400-45204000	Weak transcription	A549	lung
50	chr11:45203400-45204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links