Variant report

Variant	rs262279
Chromosome Location	chr2:180869145-180869146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180868081..180870113-chr2:205110359..205111860,2	K562	blood:
2	chr2:180868512..180871187-chr2:180902813..180905505,2	MCF-7	breast:
3	chr2:180650807..180652481-chr2:180868354..180871032,2	K562	blood:
4	chr2:180853987..180858139-chr2:180866524..180870001,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1046356	0.91[ASN][1000 genomes]
rs10497555	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613483	0.88[ASN][1000 genomes]
rs12618422	0.85[ASN][1000 genomes]
rs12621365	0.85[ASN][1000 genomes]
rs12623020	0.85[ASN][1000 genomes]
rs12693216	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16823586	0.91[ASN][1000 genomes]
rs16867114	0.91[ASN][1000 genomes]
rs16867119	0.89[ASN][1000 genomes]
rs16867125	0.93[ASN][1000 genomes]
rs16867133	0.95[ASN][1000 genomes]
rs16867136	1.00[ASN][1000 genomes]
rs16867140	0.99[ASN][1000 genomes]
rs259808	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738943	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768837	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768839	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3845695	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3845697	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845702	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3907347	0.88[ASN][1000 genomes]
rs3912257	0.96[ASN][1000 genomes]
rs3914458	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893886	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56213876	0.99[ASN][1000 genomes]
rs6433822	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6726846	0.85[ASN][1000 genomes]
rs72958832	0.85[ASN][1000 genomes]
rs72958838	0.84[ASN][1000 genomes]
rs72958887	0.91[ASN][1000 genomes]
rs72960663	0.93[ASN][1000 genomes]
rs72960669	0.94[ASN][1000 genomes]
rs72960671	0.94[ASN][1000 genomes]
rs72960679	0.92[ASN][1000 genomes]
rs818659	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989852	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1006598	chr2:180766983-180923051	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv531444	chr2:180796233-181434590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv834473	chr2:180864256-181030940	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180809400-180871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:180816800-180870600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:180819000-180871000	Weak transcription	Esophagus	oesophagus
4	chr2:180823400-180870600	Weak transcription	Fetal Intestine Small	intestine
5	chr2:180829600-180871200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:180830800-180871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:180836800-180870400	Weak transcription	A549	lung
8	chr2:180839800-180870400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:180843000-180870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:180846800-180869800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:180849000-180869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:180850600-180870800	Weak transcription	HSMMtube	muscle
13	chr2:180851000-180870200	Weak transcription	Hela-S3	cervix
14	chr2:180851600-180870400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:180851800-180870400	Weak transcription	HUVEC	blood vessel
16	chr2:180852200-180870600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:180853600-180869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:180856600-180870400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:180857200-180870000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:180857200-180870400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:180857200-180870400	Weak transcription	Thymus	Thymus
22	chr2:180857200-180871000	Weak transcription	Lung	lung
23	chr2:180857600-180869800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:180857800-180870400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:180857800-180870400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:180857800-180870600	Weak transcription	NHLF	lung
27	chr2:180857800-180870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:180857800-180870800	Weak transcription	Fetal Intestine Large	intestine
29	chr2:180858000-180869600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:180858000-180869800	Weak transcription	Adipose Nuclei	Adipose
31	chr2:180858000-180869800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:180858000-180870000	Weak transcription	Left Ventricle	heart
33	chr2:180858000-180870400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:180858000-180870400	Weak transcription	Brain Angular Gyrus	brain
35	chr2:180858000-180870400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:180858000-180870400	Weak transcription	Fetal Lung	lung
37	chr2:180858000-180870600	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:180858000-180870800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:180858200-180869600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:180858200-180869600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:180858200-180869600	Weak transcription	Osteobl	bone
42	chr2:180858200-180869800	Weak transcription	Liver	Liver
43	chr2:180858200-180870400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:180858200-180870400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:180858200-180870400	Weak transcription	Fetal Kidney	kidney
46	chr2:180858200-180870600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:180858200-180870600	Weak transcription	Fetal Thymus	thymus
48	chr2:180858200-180870600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:180858200-180870600	Weak transcription	NH-A	brain
50	chr2:180858200-180871000	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links