Variant report

Variant	rs12592319
Chromosome Location	chr15:93388388-93388389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93345885..93348752-chr15:93386057..93388854,2	MCF-7	breast:
2	chr15:93385510..93388463-chr15:93423179..93425134,2	K562	blood:
3	chr15:93385940..93388443-chr15:93390069..93391852,2	K562	blood:
4	chr15:93384664..93389325-chr15:93424657..93427477,4	MCF-7	breast:
5	chr15:93383122..93385870-chr15:93386846..93388717,2	MCF-7	breast:
6	chr15:93387429..93390014-chrX:12996770..12998336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272888	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11074108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11074109	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11074110	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11074111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591890	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28360722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28445686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28613292	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28734059	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28880667	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4408491	0.84[EUR][1000 genomes]
rs4628913	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4777740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777741	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4778045	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6496994	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180599	0.84[ASN][1000 genomes]
rs7181781	0.88[ASN][1000 genomes]
rs7184028	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes]
rs8023522	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8026478	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8027176	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8027321	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8028071	0.90[AMR][1000 genomes]
rs8029902	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8030383	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031154	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031163	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93383400-93390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:93383800-93389200	Weak transcription	Lung	lung
3	chr15:93383800-93396600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:93384000-93389200	Weak transcription	Pancreas	Pancrea
5	chr15:93384000-93394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:93384200-93389200	Weak transcription	Esophagus	oesophagus
7	chr15:93384800-93391800	Weak transcription	Placenta	Placenta
8	chr15:93385600-93388800	Enhancers	Thymus	Thymus
9	chr15:93386000-93388400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:93386000-93389600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:93386000-93389600	Enhancers	Fetal Thymus	thymus
12	chr15:93386200-93390600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:93386600-93388800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:93386600-93389400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr15:93386600-93389400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:93386600-93389800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:93386600-93390600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:93386800-93393800	Enhancers	Primary B cells from peripheral blood	blood
19	chr15:93387000-93388600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:93387200-93388400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:93387200-93388400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:93387400-93388400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:93387400-93388400	Weak transcription	Brain Germinal Matrix	brain
24	chr15:93387400-93391600	Weak transcription	Spleen	Spleen
25	chr15:93387800-93388600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr15:93387800-93389400	Enhancers	Stomach Mucosa	stomach
27	chr15:93388000-93388400	Active TSS	Colonic Mucosa	Colon
28	chr15:93388000-93388400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr15:93388000-93388400	Enhancers	Fetal Intestine Large	intestine
30	chr15:93388000-93388400	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:93388000-93388600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr15:93388000-93388600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr15:93388000-93388600	Enhancers	Adipose Nuclei	Adipose
34	chr15:93388000-93388600	Enhancers	Brain Angular Gyrus	brain
35	chr15:93388000-93388600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr15:93388000-93388600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:93388000-93388600	Enhancers	Small Intestine	intestine
38	chr15:93388000-93388600	Flanking Active TSS	HepG2	liver
39	chr15:93388000-93388600	Enhancers	HSMM	muscle
40	chr15:93388000-93388800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr15:93388000-93388800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr15:93388000-93388800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:93388000-93388800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:93388000-93388800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:93388000-93388800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:93388000-93388800	Enhancers	Brain Anterior Caudate	brain
47	chr15:93388000-93388800	Enhancers	Fetal Kidney	kidney
48	chr15:93388000-93388800	Flanking Active TSS	Dnd41	blood
49	chr15:93388000-93389000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr15:93388000-93389000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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