Variant report

Variant	rs12902857
Chromosome Location	chr15:74317871-74317872
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10162627	0.96[CEU][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs1052242	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052246	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851866	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10851867	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10851868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851869	0.90[MKK][hapmap]
rs11072458	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11072461	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11072462	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11072463	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11072464	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs11072465	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072466	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072467	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072469	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633735	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635930	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11636016	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs11636065	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636150	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854321	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11857498	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12442211	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs12592370	1.00[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12593528	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901603	0.82[AMR][1000 genomes]
rs12902945	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904213	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908748	0.83[AMR][1000 genomes]
rs12910581	0.85[AMR][1000 genomes]
rs12911807	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12911984	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917179	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2165242	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277599	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304715	0.80[AMR][1000 genomes]
rs2304716	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304717	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2304718	0.88[ASW][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784561	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784562	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4287518	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547288	0.88[ASN][1000 genomes]
rs4886820	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4886844	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886845	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886846	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56194867	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7183908	0.90[ASN][1000 genomes]
rs734854	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs743580	0.95[ASN][1000 genomes]
rs752004	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs8027327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027774	0.96[CEU][hapmap];0.82[AMR][1000 genomes]
rs8028557	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038991	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8039276	0.82[AMR][1000 genomes]
rs8039404	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8043489	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs9479	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv457203	chr15:74308940-74347723	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv569971	chr15:74308940-74347723	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
10	nsv510666	chr15:74310738-74394745	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902857	PML	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
2	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
4	chr15:74300800-74326000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:74302400-74331000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:74303600-74331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:74304000-74326000	Weak transcription	Fetal Kidney	kidney
8	chr15:74304400-74323000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:74306000-74322800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:74306400-74330600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:74309200-74322600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:74310600-74325000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:74311000-74330400	Strong transcription	GM12878-XiMat	blood
14	chr15:74311200-74323000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:74312000-74324400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:74312200-74328000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:74312800-74330600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:74313000-74321000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr15:74313000-74338600	Strong transcription	Primary T cells from cord blood	blood
20	chr15:74313200-74318600	Genic enhancers	Adipose Nuclei	Adipose
21	chr15:74313200-74320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:74313600-74330000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:74314200-74338200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:74314400-74321200	Strong transcription	Dnd41	blood
25	chr15:74314400-74330400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:74314600-74318400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:74314600-74318400	Strong transcription	Hela-S3	cervix
28	chr15:74314600-74318600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:74314600-74320400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:74314600-74320600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:74314600-74320800	Strong transcription	Fetal Intestine Small	intestine
32	chr15:74314600-74321200	Strong transcription	Primary hematopoietic stem cells	blood
33	chr15:74314600-74322400	Strong transcription	Fetal Thymus	thymus
34	chr15:74314600-74322800	Strong transcription	Thymus	Thymus
35	chr15:74314600-74330200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:74314600-74330400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:74314600-74338000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:74314800-74318200	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:74314800-74318400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:74314800-74318400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:74314800-74318600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:74314800-74318600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr15:74314800-74318600	Strong transcription	Ovary	ovary
44	chr15:74314800-74318600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:74314800-74320000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:74314800-74322600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr15:74314800-74330400	Strong transcription	NHEK	skin
48	chr15:74315000-74318200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:74315000-74318800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr15:74315000-74319000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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