Variant report

Variant	rs1596289
Chromosome Location	chr4:152410329-152410330
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152405946..152407616-chr4:152409141..152411607,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10024847	0.95[EUR][1000 genomes]
rs11099817	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11722000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723262	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726570	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729586	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732639	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735121	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930988	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11935848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11936442	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947054	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12186219	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651135	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1443088	0.89[GIH][hapmap]
rs1470280	0.89[GIH][hapmap]
rs1596291	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053566	0.89[GIH][hapmap]
rs2709810	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2709811	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2709824	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2709826	0.89[GIH][hapmap]
rs2709828	0.89[GIH][hapmap]
rs2709840	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709843	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709845	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724546	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724549	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724557	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724559	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724561	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724562	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724566	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724567	0.89[GIH][hapmap]
rs2724570	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724573	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724579	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28502777	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712546	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077562	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4309821	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4566638	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4569735	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4640653	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696098	0.87[CHB][hapmap]
rs4696099	0.87[CHB][hapmap]
rs4696264	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696265	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696268	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs55641422	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62327190	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327192	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327193	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327194	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327195	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327198	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62327258	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62329061	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6816471	0.87[CHB][hapmap]
rs6836249	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs72725968	0.84[AMR][1000 genomes]
rs72725974	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7435623	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7665216	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665950	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674244	0.86[CHB][hapmap]
rs7679642	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679829	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7683134	0.87[CHB][hapmap]
rs7695412	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs7695866	0.87[CHB][hapmap]
rs875667	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv432643	chr4:152335395-152417635	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv508321	chr4:152409994-152474456	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1596289	PET112L	cis	cerebellum	SCAN
rs1596289	SH3D19	cis	cerebellum	SCAN
rs1596289	PET112L	cis	multi-tissue	Pritchard
rs1596289	DCHS2	cis	cerebellum	SCAN
rs1596289	PET112L	cis	parietal	SCAN
rs1596289	FAM160A1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152395000-152413200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152401600-152412200	Weak transcription	Ovary	ovary
3	chr4:152403200-152412600	Weak transcription	Fetal Intestine Large	intestine
4	chr4:152406200-152410800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:152406200-152410800	Weak transcription	Hela-S3	cervix
6	chr4:152407000-152410600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:152407200-152410800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:152407200-152421600	Weak transcription	NHEK	skin
9	chr4:152407400-152410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:152407400-152410600	Weak transcription	Left Ventricle	heart
11	chr4:152407400-152413000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:152407400-152443000	Weak transcription	Pancreas	Pancrea
13	chr4:152407800-152410600	Weak transcription	Aorta	Aorta
14	chr4:152407800-152411200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:152408600-152410400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr4:152408600-152411600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr4:152408800-152411800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:152409200-152411200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:152409400-152411600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:152409600-152411800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:152409800-152411200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:152409800-152411400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr4:152410000-152410400	Enhancers	Psoas Muscle	Psoas
24	chr4:152410000-152410800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr4:152410000-152411200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:152410000-152411400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr4:152410000-152411400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr4:152410000-152411600	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr4:152410000-152411800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:152410200-152410400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:152410200-152410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:152410200-152411400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr4:152410200-152411800	Enhancers	H1 Cell Line	embryonic stem cell

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