Variant report

Variant	rs55879246
Chromosome Location	chr4:87508319-87508320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87507433..87508945-chr4:87512741..87515141,2	MCF-7	breast:
2	chr4:87507143..87508934-chr4:87512831..87514813,2	MCF-7	breast:
3	chr4:87507453..87509396-chr4:87819000..87821913,2	K562	blood:
4	chr4:87507716..87510350-chr4:87515376..87516928,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10008165	0.86[ASN][1000 genomes]
rs10023787	0.92[ASN][1000 genomes]
rs10030525	0.89[ASN][1000 genomes]
rs10031843	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1021101	0.89[ASN][1000 genomes]
rs1026861	0.85[ASN][1000 genomes]
rs11097115	0.97[ASN][1000 genomes]
rs11943428	0.90[ASN][1000 genomes]
rs11947018	0.81[ASN][1000 genomes]
rs11947775	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1481833	0.95[ASN][1000 genomes]
rs17011986	0.82[ASN][1000 genomes]
rs17418531	0.83[ASN][1000 genomes]
rs17418801	0.84[ASN][1000 genomes]
rs17418878	0.84[ASN][1000 genomes]
rs17419295	0.95[ASN][1000 genomes]
rs17419627	0.84[ASN][1000 genomes]
rs17419929	0.85[ASN][1000 genomes]
rs17452467	0.83[ASN][1000 genomes]
rs17452556	0.84[ASN][1000 genomes]
rs17453839	0.88[ASN][1000 genomes]
rs28483710	0.94[ASN][1000 genomes]
rs28485273	0.95[ASN][1000 genomes]
rs28529445	0.97[ASN][1000 genomes]
rs28534599	0.95[ASN][1000 genomes]
rs28535527	0.89[ASN][1000 genomes]
rs28663376	0.95[ASN][1000 genomes]
rs28678816	0.94[ASN][1000 genomes]
rs28735881	0.95[ASN][1000 genomes]
rs4235081	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4277747	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4405982	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4407468	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4452393	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4466012	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4511966	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4513526	0.94[ASN][1000 genomes]
rs4529013	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4552430	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4607180	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4622964	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4640633	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4693147	0.84[ASN][1000 genomes]
rs4693772	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4693776	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4693777	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55640323	0.89[ASN][1000 genomes]
rs55653332	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55654230	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55660529	0.84[ASN][1000 genomes]
rs55722156	0.84[ASN][1000 genomes]
rs55746316	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55757426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55773619	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842318	0.87[ASN][1000 genomes]
rs55872468	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55881335	0.83[ASN][1000 genomes]
rs55908925	0.87[ASN][1000 genomes]
rs55930543	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55969415	0.83[ASN][1000 genomes]
rs55978957	0.89[ASN][1000 genomes]
rs55982489	0.87[ASN][1000 genomes]
rs56009992	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56150118	0.97[ASN][1000 genomes]
rs56164000	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56178389	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56222033	0.84[ASN][1000 genomes]
rs56296936	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56348925	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56353461	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59644743	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61152200	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531932	0.92[ASN][1000 genomes]
rs66669421	0.95[ASN][1000 genomes]
rs67274037	0.95[ASN][1000 genomes]
rs67341369	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67523832	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67928053	0.94[ASN][1000 genomes]
rs6822396	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6838659	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6847139	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72664002	0.82[ASN][1000 genomes]
rs72665711	0.83[ASN][1000 genomes]
rs72665712	0.83[ASN][1000 genomes]
rs72665714	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72665719	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72665722	0.86[ASN][1000 genomes]
rs72665724	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72665725	0.86[ASN][1000 genomes]
rs72665729	0.87[ASN][1000 genomes]
rs72665734	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665736	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665737	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665738	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665740	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72665744	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665746	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72665752	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665753	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72665756	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72665759	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665762	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665769	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665771	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665772	0.97[ASN][1000 genomes]
rs72665777	0.95[ASN][1000 genomes]
rs7435744	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7673698	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7694723	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695011	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7697819	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9307020	0.95[ASN][1000 genomes]
rs9683663	0.84[ASN][1000 genomes]
rs9993042	0.97[ASN][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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87496600-87512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:87498800-87508600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:87501600-87512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:87502400-87514200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:87503800-87513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:87503800-87513800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:87504000-87508600	Weak transcription	Fetal Lung	lung
8	chr4:87504000-87513400	Weak transcription	Brain Substantia Nigra	brain
9	chr4:87506200-87509200	Enhancers	HMEC	breast
10	chr4:87506600-87508800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:87507000-87508800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr4:87507000-87508800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:87507000-87508800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:87507000-87508800	Flanking Active TSS	NHEK	skin
15	chr4:87507000-87509000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:87507000-87509200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr4:87507000-87509200	Enhancers	Fetal Intestine Large	intestine
18	chr4:87507200-87508400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:87507200-87508400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:87507200-87508600	Enhancers	Primary hematopoietic stem cells	blood
21	chr4:87507200-87509000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:87507200-87509000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr4:87507200-87509200	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr4:87507400-87508600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:87507400-87509000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:87507600-87508600	Weak transcription	Fetal Kidney	kidney
27	chr4:87507600-87508800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr4:87507600-87513200	Weak transcription	A549	lung
29	chr4:87507600-87514200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:87507800-87508600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:87508000-87508400	Active TSS	Adipose Nuclei	Adipose
32	chr4:87508000-87508600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:87508000-87508800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:87508000-87513400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:87508200-87508600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:87508200-87508600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:87508200-87508800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:87508200-87509200	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links