Variant report

Variant	rs11164050
Chromosome Location	chr2:96352451-96352452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11164049	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11676901	0.91[EUR][1000 genomes]
rs11677429	1.00[CEU][hapmap]
rs11679899	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11680743	0.85[EUR][1000 genomes]
rs11682182	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688743	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11694151	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468117	0.94[CEU][hapmap];0.85[CHB][hapmap]
rs12471472	1.00[CEU][hapmap]
rs12478605	0.92[EUR][1000 genomes]
rs1364394	1.00[CEU][hapmap]
rs1834135	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2320170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs3813663	0.91[EUR][1000 genomes]
rs4062891	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907273	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907274	0.94[EUR][1000 genomes]
rs57579941	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv998587	chr2:96170558-96378228	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv834301	chr2:96285762-96427246	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv18352	chr2:96291856-96391581	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1002700	chr2:96296630-96422939	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv874661	chr2:96334397-96459313	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv874662	chr2:96334397-96578621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv874663	chr2:96345518-96459313	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11164050	AC008268.1	cis	lung	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96349200-96353600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:96349400-96352600	Weak transcription	Ovary	ovary
3	chr2:96349400-96353600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:96349400-96356400	Weak transcription	Spleen	Spleen
5	chr2:96350400-96353400	Enhancers	Liver	Liver
6	chr2:96350400-96354400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:96351200-96354000	Enhancers	Fetal Lung	lung
8	chr2:96351200-96354200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:96351400-96354000	Enhancers	A549	lung
10	chr2:96351400-96354200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:96351600-96352600	Weak transcription	NHLF	lung
12	chr2:96351800-96352600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:96351800-96352800	Enhancers	NH-A	brain
14	chr2:96351800-96352800	Enhancers	NHEK	skin
15	chr2:96351800-96354000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:96352000-96352800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:96352000-96354000	Enhancers	HSMM	muscle
18	chr2:96352200-96352600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:96352200-96352600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:96352200-96352600	Flanking Active TSS	Osteobl	bone
21	chr2:96352200-96352800	Enhancers	Adipose Nuclei	Adipose
22	chr2:96352200-96352800	Enhancers	Gastric	stomach
23	chr2:96352200-96353000	Enhancers	Stomach Mucosa	stomach
24	chr2:96352200-96353000	Enhancers	HMEC	breast
25	chr2:96352200-96354000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:96352200-96354000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:96352200-96354400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:96352200-96354600	Enhancers	NHDF-Ad	bronchial
29	chr2:96352400-96352600	Enhancers	Pancreas	Pancrea
30	chr2:96352400-96352800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:96352400-96352800	Enhancers	Fetal Muscle Leg	muscle
32	chr2:96352400-96352800	Enhancers	HSMMtube	muscle
33	chr2:96352400-96353000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:96352400-96353000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:96352400-96353400	Enhancers	Lung	lung
36	chr2:96352400-96354000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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