Variant report

Variant	rs2665203
Chromosome Location	chr15:42316527-42316528
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	chr15:42302877..42304522-chr15:42314324..42316672,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11629515	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11633848	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11634009	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11638234	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857594	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12901016	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1622221	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs1622949	0.86[CEU][hapmap]
rs1668555	0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1668556	0.87[ASN][1000 genomes]
rs1668557	1.00[JPT][hapmap]
rs1668560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1668561	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1668562	0.88[CEU][hapmap]
rs1668567	0.87[ASN][1000 genomes]
rs1668580	0.85[ASN][1000 genomes]
rs1668581	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1668582	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1668583	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1668584	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1704353	0.87[ASN][1000 genomes]
rs1704359	0.87[ASN][1000 genomes]
rs1704362	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1704366	0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1704367	0.87[ASN][1000 genomes]
rs1704370	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs1704373	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1704376	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1823552	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2598465	0.97[ASN][1000 genomes]
rs2598466	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2598467	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665200	0.87[ASN][1000 genomes]
rs2665202	0.97[ASN][1000 genomes]
rs2665205	0.83[EUR][1000 genomes]
rs2665207	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665210	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665211	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724935	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724937	1.00[ASN][1000 genomes]
rs2724939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724940	1.00[ASN][1000 genomes]
rs2724941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724942	0.83[EUR][1000 genomes]
rs2724944	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724945	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34595238	0.87[ASN][1000 genomes]
rs35670495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55638864	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56171410	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62004270	0.87[ASN][1000 genomes]
rs7177034	1.00[YRI][hapmap]
rs937991	1.00[YRI][hapmap]
rs937992	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs937993	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv569235	chr15:42304628-42326259	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2665203	PLA2G4E	cis	cerebellum	SCAN
rs2665203	DLL4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42313200-42317600	Weak transcription	Right Atrium	heart
2	chr15:42313600-42316600	Weak transcription	Esophagus	oesophagus
3	chr15:42314000-42322400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:42314800-42317800	Weak transcription	Pancreas	Pancrea
5	chr15:42314800-42319000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:42315200-42318200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr15:42315800-42316600	Enhancers	HepG2	liver
8	chr15:42316200-42316800	Enhancers	Psoas Muscle	Psoas
9	chr15:42316200-42317000	Enhancers	Fetal Muscle Leg	muscle
10	chr15:42316400-42316600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr15:42316400-42316800	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:42316400-42316800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr15:42316400-42317200	Enhancers	Hela-S3	cervix

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