Variant report

Variant	rs1125541
Chromosome Location	chr3:151027359-151027360
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	chr3:151027323..151027838-chr3:152549309..152550012,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11708287	0.89[JPT][hapmap]
rs11715892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11717634	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487835	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494865	0.90[CEU][hapmap]
rs13088531	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13090321	0.84[EUR][1000 genomes]
rs1352886	0.84[CEU][hapmap]
rs1388627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16863323	0.90[CEU][hapmap]
rs16863334	0.84[CEU][hapmap]
rs16863336	0.84[CEU][hapmap]
rs3971192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4076581	0.85[CEU][hapmap]
rs41399847	0.82[JPT][hapmap]
rs4679794	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6793061	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1125541	GPR171	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151023200-151034600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:151023400-151027800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:151024400-151027600	Enhancers	Hela-S3	cervix
5	chr3:151024400-151029000	Genic enhancers	HMEC	breast
6	chr3:151024600-151028200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:151024600-151029600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:151024600-151032600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:151024600-151032800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:151024800-151027800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:151024800-151030200	Genic enhancers	NHEK	skin
12	chr3:151025200-151030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:151025200-151030800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:151025200-151030800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:151025200-151032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:151025400-151030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:151025600-151030800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:151025600-151032400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:151025800-151027400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:151025800-151027800	Weak transcription	Placenta	Placenta
21	chr3:151025800-151030600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:151025800-151032200	Weak transcription	Esophagus	oesophagus
23	chr3:151026000-151030600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:151026200-151030800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:151026600-151030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:151027000-151027400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:151027200-151027600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:151027200-151028000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:151027200-151030200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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