Variant report

Variant	rs882289
Chromosome Location	chr18:39855048-39855049
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	chr18:39633144..39633820-chr18:39854093..39855052,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1026595	1.00[ASN][1000 genomes]
rs1026596	1.00[ASN][1000 genomes]
rs10502780	0.92[ASN][1000 genomes]
rs11082268	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12455999	0.95[EUR][1000 genomes]
rs12457855	1.00[ASN][1000 genomes]
rs12457879	1.00[ASN][1000 genomes]
rs12457881	1.00[ASN][1000 genomes]
rs12605925	1.00[ASN][1000 genomes]
rs12956046	1.00[ASN][1000 genomes]
rs12962756	0.84[ASN][1000 genomes]
rs12967041	1.00[ASN][1000 genomes]
rs12967873	1.00[ASN][1000 genomes]
rs1381349	0.92[ASN][1000 genomes]
rs1461715	1.00[ASN][1000 genomes]
rs1461717	1.00[ASN][1000 genomes]
rs1461718	0.93[ASN][1000 genomes]
rs1461719	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1461721	0.92[ASN][1000 genomes]
rs1461723	0.91[EUR][1000 genomes]
rs1599478	0.87[EUR][1000 genomes]
rs1870781	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870782	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870783	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870785	1.00[ASN][1000 genomes]
rs2219638	0.92[ASN][1000 genomes]
rs2335779	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34703522	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35073620	0.92[ASN][1000 genomes]
rs35250842	0.86[ASN][1000 genomes]
rs35959504	0.92[ASN][1000 genomes]
rs4890391	1.00[ASN][1000 genomes]
rs4890393	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890394	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890395	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62082201	0.92[ASN][1000 genomes]
rs6507469	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7228003	0.89[EUR][1000 genomes]
rs7235905	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236024	0.92[ASN][1000 genomes]
rs7238496	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7241462	1.00[ASN][1000 genomes]
rs8085350	1.00[ASN][1000 genomes]
rs8085753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089080	0.94[EUR][1000 genomes]
rs8089100	0.92[ASN][1000 genomes]
rs882290	1.00[ASN][1000 genomes]
rs882291	1.00[ASN][1000 genomes]
rs898785	1.00[ASN][1000 genomes]
rs898786	1.00[ASN][1000 genomes]
rs898790	1.00[ASN][1000 genomes]
rs898791	1.00[ASN][1000 genomes]
rs898792	1.00[ASN][1000 genomes]
rs898793	1.00[ASN][1000 genomes]
rs898794	1.00[ASN][1000 genomes]
rs9304268	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	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1059409	chr18:39711099-40139446	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063343	chr18:39760943-39898498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	nsv1059553	chr18:39828781-39872695	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39852200-39857000	Weak transcription	Fetal Kidney	kidney
2	chr18:39854200-39855800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:39854400-39855200	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr18:39854400-39855800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr18:39854600-39855200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr18:39854600-39855400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:39854600-39855600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr18:39854600-39855600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr18:39854600-39855600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr18:39854600-39855600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr18:39854600-39855600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:39854600-39855800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr18:39854600-39855800	Enhancers	Brain Hippocampus Middle	brain
14	chr18:39854600-39857200	Enhancers	Fetal Intestine Small	intestine
15	chr18:39854800-39855200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr18:39854800-39855200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:39854800-39855400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr18:39854800-39855400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr18:39854800-39855400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr18:39854800-39855400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr18:39854800-39855400	Enhancers	Brain Anterior Caudate	brain
22	chr18:39854800-39855400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr18:39854800-39855600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr18:39854800-39855600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr18:39854800-39855800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr18:39854800-39855800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:39854800-39855800	Enhancers	Brain Cingulate Gyrus	brain
28	chr18:39854800-39855800	Enhancers	Brain Substantia Nigra	brain
29	chr18:39854800-39855800	Enhancers	Ovary	ovary
30	chr18:39854800-39855800	Enhancers	Small Intestine	intestine
31	chr18:39854800-39856000	Enhancers	Adipose Nuclei	Adipose
32	chr18:39854800-39857000	Enhancers	Fetal Intestine Large	intestine
33	chr18:39855000-39855600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr18:39855000-39855800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr18:39855000-39855800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr18:39855000-39856400	Enhancers	Fetal Heart	heart
37	chr18:39855000-39857200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links