Variant report

Variant	rs2553006
Chromosome Location	chr2:173792046-173792047
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2468389	0.91[AMR][1000 genomes]
rs2553005	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2553007	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2676499	0.91[AMR][1000 genomes]
rs2676505	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6734119	0.84[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173764400-173792600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:173769200-173792400	Weak transcription	Fetal Kidney	kidney
3	chr2:173782400-173792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:173782600-173796000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:173786200-173792400	Weak transcription	Right Atrium	heart
6	chr2:173786400-173792400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:173786400-173794800	Weak transcription	Fetal Intestine Large	intestine
8	chr2:173786600-173792200	Weak transcription	Pancreas	Pancrea
9	chr2:173786800-173792200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:173786800-173792400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:173786800-173792400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:173786800-173792600	Weak transcription	A549	lung
13	chr2:173786800-173793600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:173786800-173794600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:173786800-173794600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:173786800-173794600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:173787000-173792200	Weak transcription	Fetal Stomach	stomach
18	chr2:173787400-173792400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:173787800-173792400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:173787800-173792600	Weak transcription	Fetal Heart	heart
21	chr2:173788000-173793000	Weak transcription	HSMMtube	muscle
22	chr2:173788200-173796400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:173789000-173792400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:173789200-173799400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:173789400-173792400	Weak transcription	Fetal Lung	lung
26	chr2:173789400-173793000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:173789600-173794600	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:173789600-173795200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:173791000-173792400	Enhancers	Hela-S3	cervix
30	chr2:173791600-173792400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:173791600-173792600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:173791800-173792600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:173791800-173792600	Enhancers	Osteobl	bone
34	chr2:173791800-173792800	Enhancers	HUVEC	blood vessel
35	chr2:173791800-173793000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:173792000-173792600	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links