Variant report

Variant	rs12460804
Chromosome Location	chr19:40304040-40304041
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	chr19:40301803..40305513-chr19:40314560..40316955,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001974	0.80[CHB][hapmap]
rs10416495	1.00[ASN][1000 genomes]
rs10422280	0.81[GIH][hapmap]
rs11880094	0.81[GIH][hapmap]
rs11881344	0.82[EUR][1000 genomes]
rs12459589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs12459950	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17709688	0.83[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2072290	0.81[GIH][hapmap]
rs2354471	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810383	0.81[GIH][hapmap]
rs4802061	0.80[CHB][hapmap]
rs56021455	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56047603	0.98[ASN][1000 genomes]
rs56110449	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62106861	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62106862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106863	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718066	0.81[GIH][hapmap]
rs7247063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250408	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs7253739	0.81[GIH][hapmap]
rs7259470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507534	0.80[CHB][hapmap]
rs8111901	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12460804	PSG6	cis	cerebellum	SCAN
rs12460804	MARK4	cis	cerebellum	SCAN
rs12460804	PHLDB3	cis	parietal	SCAN
rs12460804	TOMM40	cis	cerebellum	SCAN
rs12460804	APOC4	cis	parietal	SCAN
rs12460804	PPP1R13L	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40296200-40314200	Weak transcription	Right Ventricle	heart
2	chr19:40298800-40314200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:40299800-40304200	Weak transcription	Primary T cells from cord blood	blood
4	chr19:40299800-40313600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:40300200-40314200	Weak transcription	Gastric	stomach
6	chr19:40300600-40306800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:40300800-40306600	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:40300800-40313400	Weak transcription	Pancreas	Pancrea
9	chr19:40301400-40308800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr19:40301400-40309400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr19:40301600-40306400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:40301600-40314200	Weak transcription	Ovary	ovary
13	chr19:40301600-40314400	Weak transcription	Primary B cells from cord blood	blood
14	chr19:40301600-40314400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr19:40301800-40306600	Weak transcription	A549	lung
16	chr19:40302000-40305600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:40302600-40306800	Weak transcription	Lung	lung
18	chr19:40302600-40314400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:40302800-40304800	Enhancers	Fetal Muscle Leg	muscle
20	chr19:40302800-40314200	Weak transcription	Brain Angular Gyrus	brain
21	chr19:40303000-40304800	Enhancers	Fetal Muscle Trunk	muscle
22	chr19:40303000-40314200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:40303000-40314200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr19:40303200-40314200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:40303600-40306400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:40303600-40306600	Weak transcription	Left Ventricle	heart
27	chr19:40303600-40306800	Weak transcription	Fetal Stomach	stomach
28	chr19:40303800-40304600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr19:40303800-40306600	Weak transcription	Fetal Brain Female	brain
30	chr19:40303800-40306800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:40303800-40314200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr19:40304000-40304600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:40304000-40304600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr19:40304000-40306800	Weak transcription	Psoas Muscle	Psoas
35	chr19:40304000-40313400	Weak transcription	Brain Germinal Matrix	brain
36	chr19:40304000-40314200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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