Variant report

Variant	rs28654954
Chromosome Location	chr4:16214198-16214199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16209849..16215808-chr4:16226595..16229936,7	MCF-7	breast:
2	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
3	chr4:16205687..16210095-chr4:16211514..16215415,4	K562	blood:
4	chr4:16212101..16215841-chr4:16226688..16231114,5	K562	blood:
5	chr4:16213214..16216193-chr4:16226396..16228188,2	K562	blood:

Variant related genes	Relation type
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10017532	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13120908	0.84[ASN][1000 genomes]
rs13132678	0.83[ASN][1000 genomes]
rs13136172	0.80[ASN][1000 genomes]
rs13151111	0.81[AFR][1000 genomes]
rs1373109	0.82[AFR][1000 genomes]
rs2028631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28496446	0.82[AFR][1000 genomes]
rs34496855	0.81[ASN][1000 genomes]
rs34592687	0.80[ASN][1000 genomes]
rs34663238	0.80[ASN][1000 genomes]
rs35475888	0.84[ASN][1000 genomes]
rs35517826	0.83[ASN][1000 genomes]
rs35804424	0.80[ASN][1000 genomes]
rs35806798	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35899968	0.80[ASN][1000 genomes]
rs35931597	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4235382	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4481232	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4571326	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698138	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698457	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56353092	0.80[ASN][1000 genomes]
rs6810390	0.84[ASN][1000 genomes]
rs6852432	0.84[ASN][1000 genomes]
rs73798875	0.82[AFR][1000 genomes]
rs9995025	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
3	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
4	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
5	chr4:16198600-16216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:16198800-16218800	Weak transcription	HSMM	muscle
9	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:16198800-16226000	Weak transcription	NHEK	skin
11	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:16199800-16215800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:16200000-16214200	Weak transcription	Fetal Heart	heart
14	chr4:16200800-16214800	Weak transcription	Stomach Mucosa	stomach
15	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:16204800-16226600	Weak transcription	NH-A	brain
18	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:16206400-16216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:16206400-16218400	Weak transcription	Fetal Lung	lung
21	chr4:16206600-16218400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:16207400-16216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:16208400-16214400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:16208400-16214800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:16208400-16219000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
29	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:16208800-16214400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:16208800-16214400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:16208800-16216000	Weak transcription	Psoas Muscle	Psoas
33	chr4:16208800-16216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
36	chr4:16208800-16225600	Weak transcription	Gastric	stomach
37	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:16209000-16214800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:16209000-16217000	Weak transcription	HMEC	breast
42	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:16209200-16214400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:16209200-16214800	Strong transcription	Dnd41	blood
45	chr4:16209200-16216600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle

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