Variant report

Variant	rs13005386
Chromosome Location	chr2:20316478-20316479
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	chr2:20309388..20317484-chr2:20420940..20426619,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10169811	0.90[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10171384	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10195803	0.90[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10199614	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10207632	0.85[EUR][1000 genomes]
rs10208355	0.86[CEU][hapmap]
rs1028054	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs1028055	0.90[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs11096639	0.86[CEU][hapmap]
rs11677683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677734	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679737	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11685788	0.90[CEU][hapmap]
rs11689490	0.86[CEU][hapmap]
rs11690530	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11692546	0.90[CEU][hapmap];0.80[AMR][1000 genomes]
rs11900576	0.86[CEU][hapmap]
rs13391566	0.86[CEU][hapmap]
rs34694787	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971461	0.86[EUR][1000 genomes]
rs6531203	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6531204	0.86[CEU][hapmap]
rs6531205	0.86[CEU][hapmap]
rs6531206	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs6531207	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs66598678	0.82[EUR][1000 genomes]
rs6708655	0.86[CEU][hapmap]
rs6709349	0.86[CEU][hapmap]
rs6749952	0.85[EUR][1000 genomes]
rs7556745	0.87[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs7558628	0.90[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs7561381	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7572608	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs7582437	0.86[CEU][hapmap];0.80[CHD][hapmap]
rs7583420	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs7609013	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs878983	0.81[CEU][hapmap]
rs907864	0.86[CEU][hapmap];0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3323329	chr2:20314271-20318569	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005386	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20306600-20318400	Enhancers	Placenta	Placenta
2	chr2:20306800-20318200	Weak transcription	Right Ventricle	heart
3	chr2:20308000-20322200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:20312400-20316600	Enhancers	Esophagus	oesophagus
5	chr2:20312800-20316800	Enhancers	Fetal Intestine Large	intestine
6	chr2:20313000-20316600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:20313000-20316800	Enhancers	Fetal Intestine Small	intestine
8	chr2:20313000-20317000	Enhancers	Stomach Mucosa	stomach
9	chr2:20313200-20316800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:20313400-20316600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr2:20314000-20316600	Enhancers	Gastric	stomach
12	chr2:20314200-20318000	Weak transcription	Spleen	Spleen
13	chr2:20314200-20322200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:20314800-20317000	Weak transcription	Small Intestine	intestine
15	chr2:20315000-20316800	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:20315000-20317200	Enhancers	HepG2	liver
17	chr2:20316000-20316600	Enhancers	Fetal Heart	heart
18	chr2:20316400-20322000	Weak transcription	Placenta Amnion	Placenta Amnion

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