Variant report

Variant	rs4287350
Chromosome Location	chr11:58906018-58906019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58904183..58908174-chr11:58910132..58913359,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245571	Chromatin interaction
ENSG00000166801	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10792220	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896919	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229864	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs12280905	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096543	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2845559	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4382926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939257	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs540268	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs556507	0.86[ASN][1000 genomes]
rs587617	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610764	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680661	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7939969	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4287350	LRRN4CL	cis	cerebellum	SCAN
rs4287350	OR5W2	cis	parietal	SCAN
rs4287350	BEST1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:58893800-58909600	Weak transcription	Fetal Brain Male	brain
4	chr11:58899000-58909600	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:58899600-58909600	Weak transcription	Aorta	Aorta
6	chr11:58899800-58909600	Weak transcription	Colonic Mucosa	Colon
7	chr11:58899800-58909800	Weak transcription	Gastric	stomach
8	chr11:58899800-58909800	Weak transcription	Small Intestine	intestine
9	chr11:58899800-58910000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:58900000-58909400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:58900000-58909400	Weak transcription	A549	lung
12	chr11:58900000-58909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:58900000-58909600	Weak transcription	Fetal Lung	lung
14	chr11:58900000-58910000	Weak transcription	Spleen	Spleen
15	chr11:58900600-58909400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:58901200-58909600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:58901400-58909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:58901400-58909800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:58901800-58909000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:58902200-58909000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:58902400-58909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:58902800-58908800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:58902800-58909000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:58903000-58909200	Weak transcription	HSMM	muscle
25	chr11:58903000-58909400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:58903000-58909400	Weak transcription	NHDF-Ad	bronchial
27	chr11:58903600-58909600	Weak transcription	Pancreas	Pancrea
28	chr11:58903600-58909800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:58903800-58908600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:58903800-58908600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:58903800-58908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:58903800-58908600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:58903800-58908600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:58903800-58909000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:58903800-58909000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:58903800-58909000	Weak transcription	GM12878-XiMat	blood
37	chr11:58903800-58909200	Weak transcription	Hela-S3	cervix
38	chr11:58903800-58909200	Weak transcription	HMEC	breast
39	chr11:58903800-58909400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:58903800-58909400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:58903800-58909400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:58903800-58909400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:58903800-58909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:58903800-58909400	Weak transcription	Fetal Thymus	thymus
45	chr11:58903800-58909400	Weak transcription	HUVEC	blood vessel
46	chr11:58903800-58909400	Weak transcription	NH-A	brain
47	chr11:58903800-58909600	Weak transcription	Brain Anterior Caudate	brain
48	chr11:58903800-58909600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr11:58903800-58909600	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:58903800-58909600	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links