Variant report

Variant	rs12647922
Chromosome Location	chr4:106063987-106063988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:105812145..105831361-chr4:106062414..106073665,101	MCF-7	breast:
2	chr4:106057698..106064116-chr4:106066476..106070338,7	K562	blood:
3	chr4:106061142..106064736-chr4:106066504..106068895,4	K562	blood:
4	chr4:105883010..105897017-chr4:106062943..106072055,55	MCF-7	breast:
5	chr4:105884036..105898505-chr4:106054854..106072562,138	MCF-7	breast:
6	chr17:57923944..57926540-chr4:106062604..106064911,2	MCF-7	breast:
7	chr4:106063836..106066405-chr4:106394011..106395544,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248373	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000251906	Chromatin interaction
ENSG00000168769	Chromatin interaction
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10010281	0.83[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10014102	1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs10022109	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12641113	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12643257	0.93[ASN][1000 genomes]
rs12645165	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs1391440	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17617028	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189234	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2285720	0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs35515350	0.85[EUR][1000 genomes]
rs62331150	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62331151	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974801	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9790517	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9884482	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs988799	0.83[CEU][hapmap];0.88[YRI][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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106059200-106064200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:106059400-106065600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:106061600-106064600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:106061800-106064000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:106061800-106064600	Weak transcription	Primary B cells from cord blood	blood
6	chr4:106061800-106067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:106062000-106064600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:106062000-106064800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:106062200-106067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:106062400-106064600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:106062400-106066200	Weak transcription	Fetal Lung	lung
12	chr4:106062400-106066400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:106062400-106066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:106062400-106066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:106062400-106066600	Weak transcription	Osteobl	bone
16	chr4:106062400-106066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:106062400-106066800	Weak transcription	HMEC	breast
18	chr4:106062600-106064600	Weak transcription	GM12878-XiMat	blood
19	chr4:106062600-106066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:106062600-106066200	Weak transcription	HepG2	liver
21	chr4:106062600-106066600	Weak transcription	NHEK	skin
22	chr4:106062600-106066800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:106062800-106066200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:106063600-106065200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:106063800-106065200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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