Variant report

Variant	rs2677839
Chromosome Location	chr1:84952085-84952086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84946525..84949349-chr1:84951021..84952787,2	MCF-7	breast:
2	chr1:84951639..84954302-chr1:85038478..85040171,2	K562	blood:

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11163969	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11163970	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11163979	1.00[ASN][1000 genomes]
rs11163980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163981	1.00[ASN][1000 genomes]
rs11163990	0.96[ASN][1000 genomes]
rs11163994	1.00[ASN][1000 genomes]
rs11163999	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1144276	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036957	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040469	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128801	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403545	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246159	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246236	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246253	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246254	0.94[ASN][1000 genomes]
rs1246255	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400777	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1533374	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292191	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303306	0.81[ASN][1000 genomes]
rs2389743	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659173	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794217	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794218	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911589	0.81[ASN][1000 genomes]
rs2911593	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2994954	0.89[ASN][1000 genomes]
rs2994955	0.88[ASN][1000 genomes]
rs3021402	0.87[ASN][1000 genomes]
rs312397	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312401	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906995	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4906997	0.87[ASN][1000 genomes]
rs4907078	0.94[ASN][1000 genomes]
rs6576713	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576715	0.82[ASN][1000 genomes]
rs6692765	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704211	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516200	0.92[ASN][1000 genomes]
rs7537818	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9645393	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:84946000-84956400	Weak transcription	Gastric	stomach
3	chr1:84946000-84956400	Weak transcription	Spleen	Spleen
4	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
7	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:84946200-84955200	Weak transcription	Right Ventricle	heart
10	chr1:84946200-84956200	Weak transcription	Colonic Mucosa	Colon
11	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
12	chr1:84946400-84955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:84946400-84955600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:84946400-84956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:84946400-84956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
17	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
18	chr1:84946600-84955600	Weak transcription	Brain Germinal Matrix	brain
19	chr1:84946600-84956400	Weak transcription	Psoas Muscle	Psoas
20	chr1:84946800-84955400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:84947000-84953200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:84947200-84953800	Strong transcription	Primary B cells from cord blood	blood
25	chr1:84947200-84955400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:84947200-84955600	Weak transcription	Pancreas	Pancrea
27	chr1:84947200-84955600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:84947200-84956400	Weak transcription	Brain Angular Gyrus	brain
29	chr1:84947200-84956400	Weak transcription	NHLF	lung
30	chr1:84947200-84958400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:84947400-84955000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:84947400-84955200	Weak transcription	Ovary	ovary
33	chr1:84947400-84955200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:84947400-84955200	Weak transcription	Small Intestine	intestine
35	chr1:84947400-84955800	Weak transcription	HMEC	breast
36	chr1:84947400-84957200	Weak transcription	Fetal Heart	heart
37	chr1:84947400-84957600	Weak transcription	Lung	lung
38	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
39	chr1:84947600-84952200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:84947800-84953200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:84947800-84966000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:84947800-84967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:84948000-84952800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:84948000-84953000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:84948200-84952200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:84948200-84956400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:84948400-84952200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:84948400-84952800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:84948400-84955000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:84948400-84955200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links