Variant report

Variant	rs62439778
Chromosome Location	chr6:149886122-149886123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr6:149886034-149887098	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149865611..149871097-chr6:149883709..149888968,8	K562	blood:
2	chr6:149865083..149869048-chr6:149884009..149889859,10	MCF-7	breast:
3	chr6:149885317..149886965-chr6:149968680..149971037,2	MCF-7	breast:
4	chr6:149865819..149869096-chr6:149885709..149888757,8	MCF-7	breast:
5	chr6:149871886..149874097-chr6:149885143..149886769,2	K562	blood:
6	chr6:149863889..149870301-chr6:149880315..149888361,14	K562	blood:
7	chr6:149833219..149834722-chr6:149885011..149886863,2	K562	blood:
8	chr6:149884132..149889842-chr6:149966518..149971305,10	K562	blood:
9	chr6:149884836..149889436-chr6:149966369..149971850,7	K562	blood:
10	chr6:149884840..149889202-chr6:150038504..150040931,4	K562	blood:
11	chr6:149884418..149886657-chr6:150140173..150142192,2	K562	blood:

No data

Variant related genes	Relation type
GINM1	TF binding region
ENSG00000131013	Chromatin interaction
ENSG00000186625	Chromatin interaction
ENSG00000131023	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10485097	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1125107	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12524946	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12663698	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12665533	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474640	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17732745	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2105200	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2341550	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2341551	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2341768	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28580659	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2880075	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3813675	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4869797	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4897128	0.91[EUR][1000 genomes]
rs4897131	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897132	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4897133	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897137	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4897138	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4897139	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60404985	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62442787	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62442788	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62442789	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62442790	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62442792	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442793	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442795	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442798	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570968	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6911016	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6929614	0.84[ASN][1000 genomes]
rs761617	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753560	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7774559	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7774597	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs909792	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9322184	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9322185	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9373594	0.95[EUR][1000 genomes]
rs9373595	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373596	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9377220	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377221	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377223	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377224	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390684	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9390687	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390688	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9390689	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399689	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399690	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404042	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9404043	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404044	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9406344	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9498368	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9689569	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9800648	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv966665	chr6:149862756-149895103	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62439778	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs62439778	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149884000-149886200	Enhancers	Hela-S3	cervix
2	chr6:149884200-149886200	Enhancers	NHLF	lung
3	chr6:149884400-149886200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:149884400-149886200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:149884400-149886200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:149884400-149886200	Enhancers	HMEC	breast
7	chr6:149884400-149886600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:149884400-149886600	Enhancers	HUVEC	blood vessel
9	chr6:149884600-149886200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:149884800-149886200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:149884800-149886600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:149884800-149886600	Enhancers	HSMM	muscle
13	chr6:149885200-149886200	Enhancers	Dnd41	blood
14	chr6:149885200-149886200	Bivalent Enhancer	HepG2	liver
15	chr6:149885200-149886200	Flanking Active TSS	NHEK	skin
16	chr6:149885400-149886600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:149885400-149886600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:149885400-149886600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:149885600-149886200	Weak transcription	A549	lung
20	chr6:149885600-149886400	Weak transcription	NHDF-Ad	bronchial
21	chr6:149885600-149886600	Weak transcription	Osteobl	bone
22	chr6:149885800-149886200	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:149885800-149886200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:149885800-149886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:149885800-149886400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:149885800-149888400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:149886000-149886200	Enhancers	Primary B cells from cord blood	blood
28	chr6:149886000-149886200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:149886000-149886200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:149886000-149886200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr6:149886000-149886200	Active TSS	K562	blood
32	chr6:149886000-149886400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:149886000-149886400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:149886000-149886400	Flanking Active TSS	Liver	Liver
35	chr6:149886000-149886400	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:149886000-149886600	Enhancers	NH-A	brain
37	chr6:149886000-149887600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:149886000-149888000	Active TSS	Stomach Smooth Muscle	stomach
39	chr6:149886000-149888200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr6:149886000-149888400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:149886000-149888600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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