Variant report

Variant	rs11042441
Chromosome Location	chr11:9622677-9622678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9622499..9625012-chr11:9634792..9636736,2	K562	blood:
2	chr11:9620438..9623040-chr11:9627424..9629969,2	K562	blood:
3	chr11:9616144..9619684-chr11:9621223..9625658,6	K562	blood:

Variant related genes	Relation type
ENSG00000243964	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10770044	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840287	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11042411	1.00[YRI][hapmap]
rs11042436	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042437	0.81[CEU][hapmap]
rs11042438	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042442	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042443	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042444	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042466	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[YRI][hapmap]
rs11600183	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs12422111	0.95[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap]
rs12807017	0.95[CEU][hapmap];0.86[GIH][hapmap]
rs35084800	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36084509	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4910487	0.86[CEU][hapmap]
rs7120616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7123263	0.90[EUR][1000 genomes]
rs7928738	0.86[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042441	TMEM41B	cis	parietal	SCAN
rs11042441	OR2D2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
2	chr11:9599600-9622800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:9610600-9622800	Weak transcription	Right Ventricle	heart
4	chr11:9610600-9627200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:9610600-9635000	Weak transcription	Aorta	Aorta
6	chr11:9611200-9622800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:9611400-9623400	Weak transcription	Fetal Lung	lung
8	chr11:9612000-9623200	Weak transcription	Liver	Liver
9	chr11:9612200-9622800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:9612200-9622800	Weak transcription	Fetal Intestine Small	intestine
11	chr11:9612400-9622800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:9612600-9623000	Weak transcription	HUVEC	blood vessel
13	chr11:9616200-9622800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:9616800-9622800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:9617200-9622800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:9617800-9622800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:9621800-9622800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:9621800-9623400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:9621800-9623400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:9621800-9623600	Enhancers	HMEC	breast
21	chr11:9621800-9624200	Flanking Active TSS	GM12878-XiMat	blood
22	chr11:9622000-9622800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:9622000-9622800	Enhancers	Brain Hippocampus Middle	brain
24	chr11:9622000-9622800	Weak transcription	Left Ventricle	heart
25	chr11:9622000-9623400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr11:9622000-9623600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:9622000-9623600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr11:9622000-9623600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:9622000-9623600	Enhancers	Spleen	Spleen
30	chr11:9622000-9623600	Enhancers	NHDF-Ad	bronchial
31	chr11:9622000-9624000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr11:9622200-9622800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:9622200-9622800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr11:9622200-9622800	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:9622200-9623200	Enhancers	Adipose Nuclei	Adipose
36	chr11:9622200-9623400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:9622200-9623400	Enhancers	Lung	lung
38	chr11:9622200-9623600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:9622200-9623600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:9622200-9623600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:9622200-9623600	Enhancers	Placenta	Placenta
42	chr11:9622200-9624200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:9622200-9624200	Enhancers	NHLF	lung
44	chr11:9622200-9624400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr11:9622200-9624400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:9622400-9622800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:9622400-9622800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:9622400-9622800	Enhancers	Stomach Smooth Muscle	stomach
49	chr11:9622400-9622800	Flanking Active TSS	NHEK	skin
50	chr11:9622400-9623000	Enhancers	Brain Cingulate Gyrus	brain

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