Variant report

Variant	rs12452396
Chromosome Location	chr17:59898760-59898761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59895324..59898456-chr17:59898526..59902353,6	MCF-7	breast:
2	chr12:53869484..53871513-chr17:59897576..59899229,2	MCF-7	breast:
3	chr17:59488207..59489907-chr17:59897197..59900125,2	MCF-7	breast:
4	chr17:59476100..59479841-chr17:59897699..59902465,4	MCF-7	breast:
5	chr17:59897032..59900869-chr17:59902920..59905973,5	MCF-7	breast:
6	chr17:59897823..59900768-chr17:59908892..59911351,2	MCF-7	breast:
7	chr17:59898589..59900592-chr17:59938772..59941762,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136492	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10515212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654581	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656805	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12452044	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453935	0.93[CEU][hapmap]
rs12602103	0.93[CEU][hapmap]
rs17542001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17614124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014444	0.88[CEU][hapmap]
rs2066962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278813	1.00[CEU][hapmap]
rs4968453	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4988340	0.87[CEU][hapmap]
rs56267713	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56294609	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56391142	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58426748	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504074	0.93[CEU][hapmap]
rs7223607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843728	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843731	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843735	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843752	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843757	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8075585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8076727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs8076746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
7	esv1794309	chr17:59861640-59907952	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	32 gene(s)	inside rSNPs	diseases
8	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
2	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
3	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
5	chr17:59873200-59905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:59874400-59910600	Weak transcription	Hela-S3	cervix
7	chr17:59884200-59933200	Weak transcription	K562	blood
8	chr17:59887400-59901600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:59887600-59899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:59887600-59905200	Weak transcription	Fetal Lung	lung
11	chr17:59887800-59911000	Weak transcription	NH-A	brain
12	chr17:59888000-59910400	Weak transcription	NHEK	skin
13	chr17:59888000-59911000	Weak transcription	NHLF	lung
14	chr17:59888000-59911400	Weak transcription	HSMM	muscle
15	chr17:59891000-59905200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:59891000-59911000	Weak transcription	NHDF-Ad	bronchial
17	chr17:59894000-59905200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr17:59894000-59905400	Weak transcription	HepG2	liver
19	chr17:59894000-59910600	Weak transcription	HMEC	breast
20	chr17:59894000-59922400	Weak transcription	Osteobl	bone
21	chr17:59894200-59899000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:59894800-59922000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:59896800-59899000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:59897200-59899400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:59897600-59898800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr17:59897600-59898800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:59897600-59899200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:59897600-59899400	ZNF genes & repeats	GM12878-XiMat	blood
29	chr17:59897600-59900600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:59897800-59898800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:59897800-59898800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:59897800-59899200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr17:59897800-59899400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:59897800-59900800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:59898000-59898800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:59898000-59899200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:59898000-59899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:59898000-59899400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:59898000-59899400	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr17:59898000-59899400	Strong transcription	Fetal Thymus	thymus
41	chr17:59898000-59899600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:59898200-59898800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr17:59898200-59898800	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr17:59898200-59912000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:59898400-59898800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:59898400-59898800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:59898400-59898800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:59898400-59898800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr17:59898400-59898800	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr17:59898400-59898800	ZNF genes & repeats	Thymus	Thymus

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