Variant report

Variant	rs12595160
Chromosome Location	chr15:52463485-52463486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52262525..52264741-chr15:52462329..52463854,2	MCF-7	breast:
2	chr15:52462256..52465166-chr15:52466100..52468864,2	MCF-7	breast:
3	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
4	chr15:52463285..52465150-chr15:52473016..52475731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1077383	0.85[AMR][1000 genomes]
rs11070882	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11855672	0.90[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs11856177	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438194	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs12438743	0.83[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12440956	0.83[ASN][1000 genomes]
rs12593936	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12593939	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12594679	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12594809	0.82[GIH][hapmap]
rs12901354	0.83[ASN][1000 genomes]
rs12901730	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12901891	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12902073	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap]
rs12903539	0.84[AMR][1000 genomes]
rs12903769	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12904889	0.86[ASN][1000 genomes]
rs12907835	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12908742	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12908833	0.86[ASN][1000 genomes]
rs12909161	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12909184	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12909880	0.82[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12912428	0.83[ASN][1000 genomes]
rs12916135	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916557	0.99[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap]
rs2398	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs34276836	0.82[AMR][1000 genomes]
rs34283892	1.00[ASN][1000 genomes]
rs35712143	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35827106	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794540	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3794543	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs4636859	1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4774608	0.90[ASN][1000 genomes]
rs4774612	1.00[ASW][hapmap];0.89[GIH][hapmap]
rs4776003	0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4776007	0.83[CEU][hapmap]
rs4776010	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776011	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776013	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776014	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66566761	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67163040	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67447954	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67725996	0.92[EUR][1000 genomes]
rs71472930	0.86[AFR][1000 genomes]
rs7164508	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7166799	0.84[GIH][hapmap]
rs7172037	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177248	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7183278	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8025737	0.89[GIH][hapmap];0.84[AMR][1000 genomes]
rs8029782	0.81[ASN][1000 genomes]
rs8034097	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12595160	AP4E1	cis	parietal	SCAN
rs12595160	LEO1	cis	parietal	SCAN
rs12595160	LOC100129973	cis	temporal cortex	BrainEAC
rs12595160	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs12595160	LOC100129973	cis	brain	BrainEAC

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:52439200-52463600	Weak transcription	NHEK	skin
4	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
8	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:52442600-52470400	Weak transcription	HMEC	breast
11	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:52445600-52463600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
16	chr15:52448800-52465200	Weak transcription	Liver	Liver
17	chr15:52452000-52463600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:52454200-52464000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:52454400-52463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:52455800-52463600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:52455800-52463600	Weak transcription	Primary B cells from cord blood	blood
24	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
25	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
26	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
27	chr15:52455800-52471000	Weak transcription	Gastric	stomach
28	chr15:52456000-52464800	Weak transcription	Pancreas	Pancrea
29	chr15:52456000-52468400	Weak transcription	Ovary	ovary
30	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
34	chr15:52456200-52463600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:52456200-52463600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:52456200-52467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:52456200-52468200	Weak transcription	Fetal Brain Female	brain
38	chr15:52456200-52468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
41	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
43	chr15:52462200-52464400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr15:52462600-52463800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr15:52462600-52464400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:52462600-52464400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr15:52462600-52464400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr15:52462800-52464400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr15:52463000-52463600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:52463000-52463600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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