Variant report

Variant	rs2723343
Chromosome Location	chr15:72108269-72108270
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	chr15:72097461..72102477-chr15:72104726..72109263,4	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1074330	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap]
rs11072332	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072339	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12899485	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902006	0.87[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap]
rs12903980	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916951	0.87[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs16956241	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956273	0.82[CEU][hapmap]
rs16956302	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16956328	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16956381	0.81[EUR][1000 genomes]
rs2054601	0.84[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2246225	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291278	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2625529	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2625530	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2723342	0.86[CEU][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2723356	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742323	0.90[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899773	0.80[EUR][1000 genomes]
rs3784309	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap]
rs4238447	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776579	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777464	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777467	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4777469	0.80[EUR][1000 genomes]
rs4777474	0.81[ASN][1000 genomes]
rs62023342	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8178	0.82[CEU][hapmap]
rs8747	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9120	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs972028	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972029	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2723343	TIPIN	cis	parietal	SCAN
rs2723343	SENP8	cis	cerebellum	SCAN
rs2723343	PARP6	cis	parietal	SCAN
rs2723343	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72100400-72112000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:72100600-72111000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:72100600-72113800	Weak transcription	Fetal Lung	lung
4	chr15:72100800-72111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:72101200-72112600	Weak transcription	Right Atrium	heart
6	chr15:72103400-72114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:72104800-72109800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:72105600-72112400	Weak transcription	HSMMtube	muscle
9	chr15:72105800-72109800	Weak transcription	Lung	lung
10	chr15:72106000-72114200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:72106200-72113800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:72106400-72110800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:72106800-72109600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:72106800-72114400	Weak transcription	Fetal Kidney	kidney
15	chr15:72107200-72108400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:72107200-72108600	Enhancers	Fetal Brain Male	brain
17	chr15:72107200-72108600	Enhancers	Fetal Muscle Leg	muscle
18	chr15:72107200-72115200	Weak transcription	Fetal Stomach	stomach
19	chr15:72107400-72109800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:72107600-72112000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:72107800-72115600	Weak transcription	Fetal Heart	heart
22	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain

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