Variant report

Variant	rs13428496
Chromosome Location	chr2:182647666-182647667
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182647541..182657734-chr2:182753295..182760748,23	MCF-7	breast:
2	chr2:182646086..182659083-chr2:182754079..182762654,36	MCF-7	breast:
3	chr2:182645215..182647741-chr2:182652412..182654174,2	K562	blood:

Variant related genes	Relation type
ENSG00000138434	Chromatin interaction
ENSG00000260742	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165936	0.90[AFR][1000 genomes]
rs10173114	0.95[AFR][1000 genomes]
rs10179547	0.89[AFR][1000 genomes]
rs10182213	0.89[AFR][1000 genomes]
rs10183527	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183937	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10190772	0.95[ASN][1000 genomes]
rs10803953	0.90[ASN][1000 genomes]
rs10930979	0.94[ASN][1000 genomes]
rs11884097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895376	0.95[ASN][1000 genomes]
rs11901603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902910	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424337	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425734	0.90[AFR][1000 genomes]
rs1343793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037799	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2368225	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582999	0.93[ASN][1000 genomes]
rs4018749	0.86[ASN][1000 genomes]
rs4508561	0.80[ASN][1000 genomes]
rs57930770	0.88[ASN][1000 genomes]
rs60384758	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730859	0.91[AFR][1000 genomes]
rs6740944	0.88[ASN][1000 genomes]
rs6748354	0.86[AFR][1000 genomes]
rs6754481	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567371	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7595805	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9288073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288074	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937296	0.82[ASN][1000 genomes]
rs951542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182641800-182649600	Enhancers	Fetal Intestine Large	intestine
2	chr2:182641800-182650000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:182642200-182657200	Enhancers	Hela-S3	cervix
4	chr2:182644000-182647800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:182645200-182651800	Weak transcription	Thymus	Thymus
6	chr2:182645400-182648600	Weak transcription	Osteobl	bone
7	chr2:182645400-182649200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:182645400-182649200	Weak transcription	HSMMtube	muscle
9	chr2:182645400-182649200	Weak transcription	NHDF-Ad	bronchial
10	chr2:182645400-182650600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:182645600-182649000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:182645800-182648600	Weak transcription	NH-A	brain
13	chr2:182645800-182649000	Weak transcription	HSMM	muscle
14	chr2:182646000-182648200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:182646000-182648800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:182646000-182649200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:182646000-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:182646000-182651800	Weak transcription	Fetal Thymus	thymus
19	chr2:182646200-182647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:182646200-182648600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:182646200-182648600	Weak transcription	HMEC	breast
22	chr2:182646200-182648600	Weak transcription	NHEK	skin
23	chr2:182646200-182649200	Weak transcription	Fetal Lung	lung
24	chr2:182646200-182651000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:182646400-182648000	Weak transcription	A549	lung
28	chr2:182646400-182648200	Weak transcription	Small Intestine	intestine
29	chr2:182646400-182649200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:182646400-182649200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:182646400-182650200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:182646400-182651600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:182646400-182651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:182646600-182647800	Weak transcription	Fetal Kidney	kidney
35	chr2:182646600-182648000	Weak transcription	Gastric	stomach
36	chr2:182646600-182648600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:182646600-182648600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:182646600-182651200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:182646600-182651200	Weak transcription	Pancreas	Pancrea
40	chr2:182646600-182653400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:182646600-182654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:182646800-182648800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:182647200-182648000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:182647200-182648400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:182647200-182652600	Enhancers	HepG2	liver
46	chr2:182647200-182652800	Enhancers	Stomach Mucosa	stomach
47	chr2:182647400-182647800	Enhancers	HUVEC	blood vessel
48	chr2:182647400-182648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:182647400-182648200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:182647400-182648200	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links