Variant report

Variant	rs6743339
Chromosome Location	chr2:55389689-55389690
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55384078..55385579-chr2:55388774..55390849,2	MCF-7	breast:
2	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
3	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
4	chr2:55389326..55391363-chr2:55393207..55395340,2	K562	blood:
5	chr2:55239346..55242238-chr2:55388773..55390809,2	K562	blood:
6	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:
7	chr2:55359631..55362469-chr2:55389581..55391287,2	MCF-7	breast:
8	chr2:55276196..55278592-chr2:55388732..55390265,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1134722	0.86[EUR][1000 genomes]
rs11686766	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11686912	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11687876	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12989854	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12995548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13000786	0.86[EUR][1000 genomes]
rs13003020	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13012567	0.86[EUR][1000 genomes]
rs13014752	0.87[EUR][1000 genomes]
rs13017468	0.86[EUR][1000 genomes]
rs13032294	0.95[ASN][1000 genomes]
rs2028139	0.89[EUR][1000 genomes]
rs34447956	0.86[EUR][1000 genomes]
rs35141050	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35183885	0.89[EUR][1000 genomes]
rs35227659	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35297827	0.86[EUR][1000 genomes]
rs35700883	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36121000	0.86[EUR][1000 genomes]
rs4318424	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4627623	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742306	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747466	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71414544	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414545	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414546	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414547	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414548	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414549	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71414556	0.86[EUR][1000 genomes]
rs71414557	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55381000-55391000	Enhancers	Stomach Mucosa	stomach
2	chr2:55381200-55390600	Enhancers	Brain Angular Gyrus	brain
3	chr2:55383400-55390000	Weak transcription	Fetal Kidney	kidney
4	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
5	chr2:55384000-55390600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:55384000-55392800	Weak transcription	HMEC	breast
7	chr2:55384200-55390600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:55384800-55389800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55384800-55392200	Weak transcription	Right Ventricle	heart
10	chr2:55385200-55389800	Weak transcription	Fetal Lung	lung
11	chr2:55385400-55390400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:55385400-55390600	Weak transcription	A549	lung
13	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:55386600-55389800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:55386600-55390000	Weak transcription	Ovary	ovary
16	chr2:55386600-55390400	Weak transcription	Aorta	Aorta
17	chr2:55386600-55390400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:55386600-55390600	Weak transcription	Small Intestine	intestine
19	chr2:55386600-55390600	Weak transcription	Hela-S3	cervix
20	chr2:55386800-55389800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:55386800-55389800	Weak transcription	Placenta	Placenta
22	chr2:55386800-55389800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:55386800-55389800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:55386800-55390000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:55386800-55390000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:55386800-55390000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:55386800-55390000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:55386800-55390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55386800-55390200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:55386800-55390400	Weak transcription	Fetal Stomach	stomach
31	chr2:55386800-55390800	Weak transcription	Colonic Mucosa	Colon
32	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
33	chr2:55387000-55390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:55387200-55390400	Weak transcription	Right Atrium	heart
35	chr2:55387400-55393800	Weak transcription	Fetal Heart	heart
36	chr2:55387400-55395600	Enhancers	Lung	lung
37	chr2:55387600-55390400	Weak transcription	Fetal Intestine Small	intestine
38	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
39	chr2:55387800-55389800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:55387800-55391000	Enhancers	Spleen	Spleen
41	chr2:55387800-55392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:55388000-55390400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:55388000-55391200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:55388400-55392000	Enhancers	Fetal Brain Male	brain
46	chr2:55388400-55392200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr2:55388600-55389800	Enhancers	Brain Germinal Matrix	brain
48	chr2:55388600-55390600	Enhancers	NHDF-Ad	bronchial
49	chr2:55388600-55391000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr2:55388600-55391200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links