Variant report

Variant	rs6828144
Chromosome Location	chr4:15727389-15727390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15725851..15728771-chr4:15730886..15733232,2	K562	blood:
2	chr4:15657008..15658801-chr4:15725500..15727511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10011868	1.00[CEU][hapmap]
rs10516290	1.00[CEU][hapmap]
rs10516291	1.00[CEU][hapmap]
rs1058212	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs10939630	1.00[CEU][hapmap]
rs11931532	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs11944132	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs12642189	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645693	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs12646331	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs12651490	0.82[AFR][1000 genomes]
rs16892141	1.00[CEU][hapmap]
rs16892263	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs16892271	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs16892272	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs16892276	1.00[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs16892283	1.00[CEU][hapmap]
rs16892287	1.00[CEU][hapmap]
rs16892289	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs16898413	1.00[CEU][hapmap]
rs2302463	1.00[CEU][hapmap]
rs2302464	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs35016714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097300	0.86[AFR][1000 genomes]
rs4267735	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4321629	1.00[CEU][hapmap]
rs4395498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4435745	1.00[CEU][hapmap]
rs4498133	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs4502676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57326588	0.86[AFR][1000 genomes]
rs57497036	0.86[AFR][1000 genomes]
rs57987867	0.86[AFR][1000 genomes]
rs58156049	0.82[EUR][1000 genomes]
rs58978163	0.84[AFR][1000 genomes]
rs60913985	0.86[AFR][1000 genomes]
rs6811179	1.00[CEU][hapmap]
rs6835705	1.00[CEU][hapmap]
rs6844968	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs73121395	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73123607	0.86[AFR][1000 genomes]
rs73123615	0.86[AFR][1000 genomes]
rs7672395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7688526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs955410	1.00[CEU][hapmap]
rs9790670	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs9942211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9942247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9942275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15705000-15735200	Weak transcription	Lung	lung
2	chr4:15705200-15731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:15705400-15727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:15706000-15727800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
6	chr4:15708800-15739400	Weak transcription	Ovary	ovary
7	chr4:15709400-15731800	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:15716800-15727600	Weak transcription	Brain Anterior Caudate	brain
9	chr4:15719400-15735800	Weak transcription	NHDF-Ad	bronchial
10	chr4:15719800-15736600	Weak transcription	Spleen	Spleen
11	chr4:15720200-15727400	Strong transcription	Fetal Intestine Large	intestine
12	chr4:15720600-15729000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr4:15721000-15728800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:15721000-15729600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:15721400-15728800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:15723000-15734600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:15723000-15743000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:15723000-15744600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:15724000-15732000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:15724600-15730200	Weak transcription	Fetal Intestine Small	intestine
21	chr4:15725600-15727400	Strong transcription	NH-A	brain
22	chr4:15726000-15727600	Weak transcription	HepG2	liver
23	chr4:15726000-15730000	Weak transcription	Adipose Nuclei	Adipose
24	chr4:15726000-15731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:15726000-15737400	Weak transcription	NHLF	lung
26	chr4:15726000-15740200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:15726400-15727400	Enhancers	Rectal Smooth Muscle	rectum
28	chr4:15726400-15727800	Enhancers	Fetal Stomach	stomach
29	chr4:15726400-15728000	Enhancers	Thymus	Thymus
30	chr4:15726600-15727400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:15726600-15728200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:15726600-15728200	Enhancers	Colon Smooth Muscle	Colon
33	chr4:15726800-15727800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:15726800-15729000	Enhancers	Fetal Thymus	thymus
35	chr4:15727000-15727400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr4:15727000-15728000	Enhancers	Osteobl	bone
37	chr4:15727200-15727400	Enhancers	Colonic Mucosa	Colon
38	chr4:15727200-15731800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:15727200-15732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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