Variant report

Variant	rs11042466
Chromosome Location	chr11:9686800-9686801
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9681496..9684327-chr11:9685314..9687599,2	K562	blood:
2	chr11:9635657..9637159-chr11:9686246..9687885,2	MCF-7	breast:
3	chr11:9686212..9687839-chr11:9688386..9690328,2	K562	blood:
4	chr11:9686339..9687922-chr11:9688828..9691707,2	K562	blood:
5	chr11:9681661..9684327-chr11:9686099..9688076,2	K562	blood:

Variant related genes	Relation type
ENSG00000239470	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10770044	0.82[CEU][hapmap]
rs10770051	0.83[EUR][1000 genomes]
rs10840283	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840284	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840285	0.83[CEU][hapmap]
rs10840286	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840287	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042411	1.00[YRI][hapmap]
rs11042439	1.00[ASW][hapmap];0.91[CEU][hapmap]
rs11042440	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[YRI][hapmap]
rs11042441	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[YRI][hapmap]
rs11042457	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042462	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042464	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042467	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042486	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042500	1.00[CHB][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11600183	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11601008	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603527	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11607321	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607776	0.85[EUR][1000 genomes]
rs11607900	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362879	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364089	1.00[ASN][1000 genomes]
rs12421878	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12786236	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12789209	1.00[ASN][1000 genomes]
rs12789429	1.00[ASN][1000 genomes]
rs12794270	1.00[ASN][1000 genomes]
rs12797744	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12801958	1.00[ASN][1000 genomes]
rs12803440	1.00[ASN][1000 genomes]
rs12805683	1.00[ASN][1000 genomes]
rs12807017	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs17268632	1.00[CHB][hapmap]
rs34063054	1.00[ASN][1000 genomes]
rs35806232	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089180	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910060	1.00[ASN][1000 genomes]
rs4910486	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910487	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910488	1.00[ASN][1000 genomes]
rs4910492	1.00[ASN][1000 genomes]
rs4910493	1.00[ASN][1000 genomes]
rs4910497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4910505	1.00[CHB][hapmap]
rs56043731	1.00[ASN][1000 genomes]
rs67867011	1.00[ASN][1000 genomes]
rs7120616	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs72852112	1.00[ASN][1000 genomes]
rs7943610	1.00[CHB][hapmap]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11042466	OR2D2	cis	cerebellum	SCAN
rs11042466	COL25A1	trans	cerebellum	SCAN
rs11042466	TMEM41B	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9684400-9686800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:9684800-9686800	Active TSS	Aorta	Aorta
3	chr11:9684800-9687000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr11:9684800-9687000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:9684800-9687000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr11:9684800-9687000	Active TSS	Brain Cingulate Gyrus	brain
7	chr11:9684800-9687200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr11:9684800-9687200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr11:9684800-9687200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr11:9684800-9687200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr11:9684800-9687200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:9684800-9687200	Active TSS	Brain Hippocampus Middle	brain
13	chr11:9684800-9687200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr11:9684800-9687200	Active TSS	Right Atrium	heart
15	chr11:9684800-9687400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr11:9684800-9687400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr11:9684800-9687400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:9684800-9687400	Active TSS	Rectal Smooth Muscle	rectum
19	chr11:9684800-9687800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr11:9685000-9686800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:9685000-9686800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:9685000-9686800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr11:9685000-9686800	Active TSS	Brain Angular Gyrus	brain
24	chr11:9685000-9686800	Active TSS	Ovary	ovary
25	chr11:9685000-9687000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr11:9685000-9687000	Active TSS	Fetal Intestine Small	intestine
27	chr11:9685000-9687000	Active TSS	Fetal Kidney	kidney
28	chr11:9685000-9687000	Active TSS	Right Ventricle	heart
29	chr11:9685000-9687200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr11:9685000-9687200	Active TSS	Fetal Lung	lung
31	chr11:9685000-9687200	Active TSS	Lung	lung
32	chr11:9685000-9687200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr11:9685000-9687200	Active TSS	NHDF-Ad	bronchial
34	chr11:9685000-9687400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:9685200-9686800	Active TSS	Brain Substantia Nigra	brain
36	chr11:9685200-9686800	Active TSS	Stomach Mucosa	stomach
37	chr11:9685200-9686800	Active TSS	A549	lung
38	chr11:9685200-9687000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:9685200-9687000	Active TSS	Brain Anterior Caudate	brain
40	chr11:9685200-9687000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr11:9685200-9687200	Active TSS	Fetal Intestine Large	intestine
42	chr11:9685200-9687400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr11:9685200-9687400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr11:9685200-9687600	Active TSS	Fetal Heart	heart
45	chr11:9685200-9688800	Active TSS	GM12878-XiMat	blood
46	chr11:9685400-9686800	Active TSS	HUVEC	blood vessel
47	chr11:9685400-9687000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:9685400-9687000	Active TSS	Primary T cells from cord blood	blood
49	chr11:9685400-9687000	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr11:9685400-9687000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links