Variant report

Variant	rs2657932
Chromosome Location	chr19:52787453-52787454
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52786937..52789326-chr19:52800045..52802285,2	MCF-7	breast:
2	chr19:52786877..52789123-chr19:52793597..52795383,2	K562	blood:
3	chr19:52774375..52777116-chr19:52786827..52789950,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10416012	0.85[CEU][hapmap]
rs10520481	1.00[JPT][hapmap]
rs12462518	0.92[EUR][1000 genomes]
rs13344871	0.87[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs16983537	1.00[JPT][hapmap]
rs16983625	1.00[JPT][hapmap]
rs16983630	1.00[JPT][hapmap]
rs2002322	1.00[JPT][hapmap]
rs2434422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657929	1.00[JPT][hapmap]
rs28480595	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs321907	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs321908	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs321927	0.85[CEU][hapmap]
rs57523152	0.92[EUR][1000 genomes]
rs62110364	0.92[EUR][1000 genomes]
rs6509631	0.85[CEU][hapmap]
rs7249460	1.00[JPT][hapmap]
rs7251497	1.00[JPT][hapmap]
rs7251582	0.92[EUR][1000 genomes]
rs7251605	1.00[JPT][hapmap]
rs7253555	0.85[CEU][hapmap]
rs8107383	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS 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	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
3	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:52777200-52794000	Weak transcription	Psoas Muscle	Psoas
5	chr19:52777800-52787800	Weak transcription	HMEC	breast
6	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:52781600-52793600	Weak transcription	Fetal Heart	heart
8	chr19:52783000-52787600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:52783200-52794800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:52783200-52795200	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr19:52783400-52795800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
12	chr19:52784400-52788200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:52784400-52794800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:52784600-52791600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:52784600-52792000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:52784600-52794000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:52784600-52794600	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr19:52784600-52795000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
19	chr19:52784600-52795800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:52784600-52796000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:52784600-52796400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:52784600-52796800	ZNF genes & repeats	Liver	Liver
23	chr19:52784800-52789800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:52784800-52790000	Strong transcription	Fetal Brain Female	brain
25	chr19:52784800-52790200	ZNF genes & repeats	GM12878-XiMat	blood
26	chr19:52784800-52790800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:52784800-52793400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:52784800-52794800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:52784800-52795800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:52784800-52795800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:52784800-52795800	Strong transcription	Dnd41	blood
32	chr19:52785000-52787600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:52785000-52793600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:52785000-52795400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr19:52785000-52795800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:52785000-52796000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:52785200-52789800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:52785200-52792000	Strong transcription	Fetal Lung	lung
39	chr19:52785200-52794600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:52785200-52794800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:52785200-52795400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:52785200-52796000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:52785200-52796400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:52785400-52787600	Strong transcription	Primary B cells from cord blood	blood
45	chr19:52785400-52788200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:52785400-52788600	Strong transcription	Fetal Muscle Leg	muscle
47	chr19:52785400-52789200	Strong transcription	Gastric	stomach
48	chr19:52785400-52789400	Strong transcription	Aorta	Aorta
49	chr19:52785400-52790200	Strong transcription	Fetal Stomach	stomach
50	chr19:52785400-52794200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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