Variant report

Variant	rs882290
Chromosome Location	chr18:39854956-39854957
allele	A/G
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: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1026595	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026596	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11082268	1.00[ASN][1000 genomes]
rs12457855	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457879	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12605925	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956046	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12962756	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12967041	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381349	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1461715	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461717	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461718	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1461719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1461721	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870781	1.00[ASN][1000 genomes]
rs1870782	1.00[ASN][1000 genomes]
rs1870783	1.00[ASN][1000 genomes]
rs1870785	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219638	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2335779	1.00[ASN][1000 genomes]
rs34703522	0.93[ASN][1000 genomes]
rs35073620	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35250842	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35959504	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4890391	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890393	1.00[ASN][1000 genomes]
rs4890394	1.00[ASN][1000 genomes]
rs4890395	1.00[ASN][1000 genomes]
rs62082201	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507469	0.92[ASN][1000 genomes]
rs7235905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7236024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7238496	0.92[ASN][1000 genomes]
rs7241462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085350	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085753	1.00[ASN][1000 genomes]
rs8089100	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs882289	1.00[ASN][1000 genomes]
rs882291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898785	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898786	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898791	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898793	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898794	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304268	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[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	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39852200-39857000	Weak transcription	Fetal Kidney	kidney
2	chr18:39852400-39855000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:39854200-39855800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:39854400-39855200	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr18:39854400-39855800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr18:39854600-39855200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr18:39854600-39855400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:39854600-39855600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr18:39854600-39855600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr18:39854600-39855600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr18:39854600-39855600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr18:39854600-39855600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:39854600-39855800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr18:39854600-39855800	Enhancers	Brain Hippocampus Middle	brain
15	chr18:39854600-39857200	Enhancers	Fetal Intestine Small	intestine
16	chr18:39854800-39855000	Enhancers	Duodenum Mucosa	Duodenum
17	chr18:39854800-39855200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr18:39854800-39855200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:39854800-39855400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr18:39854800-39855400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:39854800-39855400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr18:39854800-39855400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr18:39854800-39855400	Enhancers	Brain Anterior Caudate	brain
24	chr18:39854800-39855400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr18:39854800-39855600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr18:39854800-39855600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr18:39854800-39855800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr18:39854800-39855800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr18:39854800-39855800	Enhancers	Brain Cingulate Gyrus	brain
30	chr18:39854800-39855800	Enhancers	Brain Substantia Nigra	brain
31	chr18:39854800-39855800	Enhancers	Ovary	ovary
32	chr18:39854800-39855800	Enhancers	Small Intestine	intestine
33	chr18:39854800-39856000	Enhancers	Adipose Nuclei	Adipose
34	chr18:39854800-39857000	Enhancers	Fetal Intestine Large	intestine

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