Variant report

Variant	rs12593936
Chromosome Location	chr15:52469181-52469182
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr15:52469143-52469221	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52465292..52467167-chr15:52468410..52470293,2	MCF-7	breast:
2	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
3	chr15:52469037..52470714-chr15:52511840..52513591,2	MCF-7	breast:
4	chr15:52464249..52467192-chr15:52469129..52471507,3	K562	blood:

Variant related genes	Relation type
ENSG00000259577	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1077383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11070882	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11855672	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11856177	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438743	0.80[MEX][hapmap]
rs12593939	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595160	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]
rs12902522	1.00[CEU][hapmap]
rs12903539	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12916135	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34276836	0.84[ASN][1000 genomes]
rs35712143	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35827106	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4774612	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs4776003	0.81[MEX][hapmap]
rs4776010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776011	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776013	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776014	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66566761	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67163040	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67447954	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67725996	0.94[EUR][1000 genomes]
rs7164508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172037	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183278	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8025737	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12593936	BCL2L10	cis	parietal	SCAN
rs12593936	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs12593936	GNB5	cis	multi-tissue	Pritchard
rs12593936	LEO1	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52442600-52470400	Weak transcription	HMEC	breast
7	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
10	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
12	chr15:52455800-52471000	Weak transcription	Gastric	stomach
13	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
17	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
19	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
21	chr15:52463200-52470600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:52463600-52470400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:52463800-52470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:52464000-52469600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:52464000-52470000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:52464000-52470200	Weak transcription	NHEK	skin
27	chr15:52464000-52470800	Weak transcription	HUVEC	blood vessel
28	chr15:52464000-52471000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:52464200-52469800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:52464200-52470200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:52464200-52470400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:52464400-52470000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:52464400-52470000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:52464400-52470200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:52464400-52470400	Weak transcription	Primary T cells from cord blood	blood
36	chr15:52464400-52470600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:52464400-52470600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:52464800-52470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:52465600-52470600	Weak transcription	Liver	Liver
40	chr15:52465800-52470600	Weak transcription	Pancreas	Pancrea
41	chr15:52467200-52469200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:52467200-52470000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:52467400-52470600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:52467600-52470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:52468200-52469200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:52468400-52469200	Active TSS	Brain Anterior Caudate	brain
47	chr15:52468400-52469200	Enhancers	Brain Germinal Matrix	brain
48	chr15:52468400-52469200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr15:52468400-52469600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:52468400-52470800	Genic enhancers	Primary B cells from peripheral blood	blood

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