Variant report

Variant	rs340635
Chromosome Location	chr4:87931404-87931405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87867281..87868896-chr4:87929541..87932174,2	MCF-7	breast:
2	chr4:87929393..87932319-chr4:87992706..87994245,2	K562	blood:
3	chr4:87925144..87930778-chr4:87931161..87934688,7	MCF-7	breast:
4	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
5	chr12:57480398..57483000-chr4:87931079..87932679,2	MCF-7	breast:
6	chr4:87929301..87933851-chr4:88000404..88005339,4	K562	blood:
7	chr4:87854689..87857093-chr4:87930959..87933070,3	MCF-7	breast:
8	chr4:87832559..87834802-chr4:87929759..87932272,2	K562	blood:
9	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000235043	Chromatin interaction
ENSG00000172493	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10003332	0.92[ASN][1000 genomes]
rs10008600	0.95[ASN][1000 genomes]
rs10022960	0.92[ASN][1000 genomes]
rs1374936	0.83[ASN][1000 genomes]
rs1374937	0.83[ASN][1000 genomes]
rs168161	1.00[ASN][1000 genomes]
rs17012291	0.97[ASN][1000 genomes]
rs1972969	1.00[ASN][1000 genomes]
rs2053772	0.95[ASN][1000 genomes]
rs2053774	0.91[ASN][1000 genomes]
rs2272777	0.97[ASN][1000 genomes]
rs2705617	0.83[ASN][1000 genomes]
rs340627	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340628	0.97[ASN][1000 genomes]
rs340629	0.97[ASN][1000 genomes]
rs340631	1.00[ASN][1000 genomes]
rs340632	0.96[ASN][1000 genomes]
rs340640	0.97[ASN][1000 genomes]
rs340644	0.97[ASN][1000 genomes]
rs340645	0.97[ASN][1000 genomes]
rs340646	0.92[ASN][1000 genomes]
rs340647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340649	1.00[ASN][1000 genomes]
rs340652	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536897	0.92[ASN][1000 genomes]
rs4693155	1.00[ASN][1000 genomes]
rs4693797	0.95[ASN][1000 genomes]
rs4693799	1.00[ASN][1000 genomes]
rs58317309	0.93[ASN][1000 genomes]
rs6531943	0.97[ASN][1000 genomes]
rs6531944	1.00[ASN][1000 genomes]
rs6531945	1.00[ASN][1000 genomes]
rs6531947	0.97[ASN][1000 genomes]
rs6815546	0.95[ASN][1000 genomes]
rs6848056	0.92[ASN][1000 genomes]
rs6853011	0.92[ASN][1000 genomes]
rs73837575	0.97[ASN][1000 genomes]
rs895740	0.83[ASN][1000 genomes]
rs965824	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alzheimer's disease (cognitive decline)	23535033	GWAS catalog

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87927600-87932200	Active TSS	GM12878-XiMat	blood
2	chr4:87928800-87931800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr4:87928800-87931800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:87929200-87931600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:87929200-87934200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:87929200-87939400	Weak transcription	Gastric	stomach
7	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
8	chr4:87929600-87931600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:87929600-87931600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:87929600-87931600	Enhancers	Stomach Mucosa	stomach
11	chr4:87929600-87932200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:87929600-87932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:87929600-87933200	Enhancers	Brain Substantia Nigra	brain
14	chr4:87929600-87934000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:87929600-87935000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:87929600-87935400	Weak transcription	HSMM	muscle
17	chr4:87929600-87937000	Enhancers	Fetal Heart	heart
18	chr4:87929600-87938000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr4:87929600-87938800	Weak transcription	HSMMtube	muscle
20	chr4:87929800-87932000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:87929800-87932400	Weak transcription	NH-A	brain
22	chr4:87929800-87932600	Enhancers	A549	lung
23	chr4:87929800-87933600	Enhancers	HepG2	liver
24	chr4:87929800-87936600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:87929800-87937000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:87930000-87932000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr4:87930000-87932000	Enhancers	Brain Cingulate Gyrus	brain
28	chr4:87930000-87932400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:87930000-87932400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:87930200-87931600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:87930200-87932000	Flanking Active TSS	K562	blood
32	chr4:87930200-87932800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:87930200-87933000	Enhancers	Small Intestine	intestine
34	chr4:87930200-87933400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:87930400-87931600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr4:87930400-87931800	Enhancers	Fetal Lung	lung
37	chr4:87930400-87932400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:87930400-87932600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:87930600-87932400	Weak transcription	Osteobl	bone
40	chr4:87930600-87932600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:87930600-87934000	Enhancers	Fetal Intestine Small	intestine
42	chr4:87930600-87934400	Weak transcription	Pancreas	Pancrea
43	chr4:87930600-87934600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:87930600-87937000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:87930600-87940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
48	chr4:87930800-87931800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:87930800-87931800	Enhancers	Brain Hippocampus Middle	brain
50	chr4:87930800-87931800	Weak transcription	Left Ventricle	heart

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