Variant report

Variant	rs62410132
Chromosome Location	chr4:20723715-20723716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20701205..20703695-chr4:20723209..20725454,2	MCF-7	breast:
2	chr4:20700788..20703573-chr4:20723140..20724857,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10516361	1.00[ASN][1000 genomes]
rs1061836	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1080125	0.88[ASN][1000 genomes]
rs11721944	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723855	0.89[ASN][1000 genomes]
rs11733451	0.88[ASN][1000 genomes]
rs11735866	0.86[ASN][1000 genomes]
rs11736309	0.88[ASN][1000 genomes]
rs11736477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737893	0.92[ASN][1000 genomes]
rs12498799	0.88[ASN][1000 genomes]
rs12503714	1.00[ASN][1000 genomes]
rs12509329	0.90[ASN][1000 genomes]
rs12510666	0.94[ASN][1000 genomes]
rs1365580	0.96[ASN][1000 genomes]
rs1365581	0.96[ASN][1000 genomes]
rs1426882	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869823	0.86[ASN][1000 genomes]
rs16869859	1.00[ASN][1000 genomes]
rs16869884	1.00[ASN][1000 genomes]
rs17552950	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622121	0.92[ASN][1000 genomes]
rs2291530	0.89[ASN][1000 genomes]
rs28439580	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267013	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57364495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59020971	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61790721	0.86[ASN][1000 genomes]
rs61790747	0.86[ASN][1000 genomes]
rs62410066	0.92[ASN][1000 genomes]
rs62410087	0.92[ASN][1000 genomes]
rs62410133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410158	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411661	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831523	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73101456	0.92[ASN][1000 genomes]
rs964020	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62410132	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
2	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:20703400-20724000	Weak transcription	A549	lung
4	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
5	chr4:20707200-20724000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:20707200-20739400	Weak transcription	HepG2	liver
7	chr4:20707600-20724000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:20707600-20724000	Weak transcription	NHEK	skin
9	chr4:20707600-20724000	Weak transcription	NHLF	lung
10	chr4:20708000-20724000	Weak transcription	HMEC	breast
11	chr4:20708200-20733600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:20709400-20724200	Weak transcription	HUVEC	blood vessel
13	chr4:20712600-20724000	Weak transcription	HSMM	muscle
14	chr4:20715200-20724000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:20715200-20724000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:20715400-20724000	Weak transcription	K562	blood
17	chr4:20715400-20738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:20715400-20739400	Weak transcription	Osteobl	bone
19	chr4:20717800-20724200	Weak transcription	NH-A	brain
20	chr4:20718000-20738600	Weak transcription	NHDF-Ad	bronchial
21	chr4:20718200-20724000	Weak transcription	Fetal Brain Male	brain
22	chr4:20718200-20724000	Weak transcription	HSMMtube	muscle
23	chr4:20718200-20738400	Weak transcription	Fetal Heart	heart
24	chr4:20721600-20727600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:20721800-20724000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr4:20721800-20724400	ZNF genes & repeats	Fetal Brain Female	brain
27	chr4:20721800-20724800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:20721800-20724800	Strong transcription	Rectal Smooth Muscle	rectum
29	chr4:20721800-20725200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:20721800-20725600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:20721800-20736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:20721800-20736400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:20721800-20737200	Strong transcription	Liver	Liver
34	chr4:20722000-20723800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:20722000-20724000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr4:20722000-20724400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr4:20722000-20724400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:20722000-20724400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr4:20722000-20724600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:20722000-20724600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:20722000-20724600	Strong transcription	Fetal Kidney	kidney
42	chr4:20722000-20724800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
43	chr4:20722000-20724800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
44	chr4:20722000-20724800	Strong transcription	Primary T cells from cord blood	blood
45	chr4:20722000-20724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:20722000-20724800	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr4:20722000-20725000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:20722000-20725000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:20722000-20725200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
50	chr4:20722000-20725400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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