Variant report

Variant	rs13396958
Chromosome Location	chr2:189962360-189962361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10165488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10166835	1.00[YRI][hapmap]
rs10166867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10168625	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10172837	1.00[YRI][hapmap]
rs10176299	1.00[AMR][1000 genomes]
rs10180374	1.00[AMR][1000 genomes]
rs10182790	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10182959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190048	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10193357	1.00[AMR][1000 genomes]
rs10195176	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10196855	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10202897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10203522	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10207418	1.00[YRI][hapmap]
rs10210715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13382234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383366	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13383588	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13385646	1.00[YRI][hapmap]
rs13385828	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13389070	1.00[AMR][1000 genomes]
rs13392441	1.00[AMR][1000 genomes]
rs13392501	1.00[YRI][hapmap]
rs13395385	1.00[AMR][1000 genomes]
rs13395712	1.00[YRI][hapmap]
rs13401632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405822	1.00[AFR][1000 genomes]
rs13405825	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13407402	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13408124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411571	1.00[AFR][1000 genomes]
rs13411962	1.00[AMR][1000 genomes]
rs13413060	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13413296	1.00[AFR][1000 genomes]
rs13414033	1.00[YRI][hapmap]
rs13416565	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419998	1.00[AMR][1000 genomes]
rs13420752	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13421412	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13430867	1.00[AMR][1000 genomes]
rs13431520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13433016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28712861	1.00[AMR][1000 genomes]
rs28763874	1.00[AMR][1000 genomes]
rs28763875	1.00[AMR][1000 genomes]
rs59459440	1.00[AMR][1000 genomes]
rs6712385	1.00[AMR][1000 genomes]
rs6732228	1.00[AMR][1000 genomes]
rs73981448	1.00[AMR][1000 genomes]
rs73981451	1.00[AMR][1000 genomes]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv3074	chr2:189931263-189976124	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
3	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:189922800-189980800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:189933000-189980200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:189936600-189969200	Weak transcription	Liver	Liver
7	chr2:189941200-189975000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:189947600-189980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:189948200-189980600	Weak transcription	Placenta	Placenta
10	chr2:189948600-189974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:189950800-189977800	Weak transcription	Fetal Intestine Large	intestine
12	chr2:189954800-189980400	Weak transcription	Ovary	ovary
13	chr2:189956800-189962600	Genic enhancers	HSMM	muscle
14	chr2:189958000-189968000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:189958200-189981000	Weak transcription	Fetal Stomach	stomach
16	chr2:189959400-189962600	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:189959400-189963200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:189959600-189962800	Genic enhancers	Muscle Satellite Cultured Cells	--
19	chr2:189960200-189962800	Enhancers	HUVEC	blood vessel
20	chr2:189960200-189973800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:189960400-189974400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:189960800-189962800	Weak transcription	Fetal Lung	lung
23	chr2:189960800-189967600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:189961200-189962400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:189961200-189963000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:189961200-189963400	Strong transcription	Adipose Nuclei	Adipose
27	chr2:189961400-189962600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:189961400-189962600	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:189961400-189963200	Genic enhancers	NHDF-Ad	bronchial
30	chr2:189961600-189962400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:189961600-189962600	Enhancers	Colon Smooth Muscle	Colon
32	chr2:189961600-189963000	Genic enhancers	NHLF	lung
33	chr2:189961600-189963800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:189961800-189962400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:189961800-189962400	Enhancers	Aorta	Aorta
36	chr2:189961800-189962400	Enhancers	HSMMtube	muscle
37	chr2:189961800-189963000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:189962000-189962400	Flanking Active TSS	A549	lung
39	chr2:189962000-189962400	Genic enhancers	Osteobl	bone
40	chr2:189962000-189962600	Enhancers	Fetal Heart	heart
41	chr2:189962000-189962600	Genic enhancers	NH-A	brain
42	chr2:189962200-189963000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:189962200-189964200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:189962200-189973600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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