Variant report

Variant	rs340640
Chromosome Location	chr4:87952589-87952590
allele	A/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	chr4:87944178..87948145-chr4:87950244..87953545,6	K562	blood:
2	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
3	chr4:87946350..87948006-chr4:87951593..87953106,2	MCF-7	breast:
4	chr4:87951686..87953695-chr4:87963099..87965280,2	K562	blood:
5	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
6	chr4:87926723..87929502-chr4:87950750..87952637,2	MCF-7	breast:
7	chr4:87926472..87930256-chr4:87951394..87957719,6	K562	blood:
8	chr20:46131389..46132897-chr4:87950078..87952930,2	MCF-7	breast:
9	chr4:87854933..87857678-chr4:87950865..87954006,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10003332	0.89[ASN][1000 genomes]
rs10008600	0.92[ASN][1000 genomes]
rs10022960	0.89[ASN][1000 genomes]
rs1374936	0.80[ASN][1000 genomes]
rs1374937	0.80[ASN][1000 genomes]
rs168161	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012291	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972969	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053772	0.92[ASN][1000 genomes]
rs2053774	0.88[ASN][1000 genomes]
rs2272777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705617	0.80[ASN][1000 genomes]
rs340627	1.00[ASN][1000 genomes]
rs340628	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340629	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340631	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340632	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340635	0.97[ASN][1000 genomes]
rs340644	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340645	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340646	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340647	0.95[ASN][1000 genomes]
rs340649	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340652	0.97[ASN][1000 genomes]
rs4536897	0.89[ASN][1000 genomes]
rs4693155	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693797	0.92[ASN][1000 genomes]
rs4693799	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317309	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531943	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531944	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815546	0.92[ASN][1000 genomes]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.89[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895740	0.80[ASN][1000 genomes]
rs965824	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87944200-87953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
4	chr4:87947800-87957200	Weak transcription	Dnd41	blood
5	chr4:87948000-87954200	Weak transcription	A549	lung
6	chr4:87949200-87957400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:87949200-87961000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:87949400-87960600	Enhancers	Liver	Liver
9	chr4:87949600-87954000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr4:87949600-87955600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:87949600-87960800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:87949800-87953200	Enhancers	HUVEC	blood vessel
13	chr4:87949800-87957400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:87949800-87960800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:87950000-87952600	Enhancers	Right Ventricle	heart
16	chr4:87950000-87953200	Enhancers	Duodenum Mucosa	Duodenum
17	chr4:87950000-87953200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:87950000-87954000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr4:87950000-87954400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:87950000-87955600	Enhancers	Fetal Stomach	stomach
21	chr4:87950000-87955600	Enhancers	Small Intestine	intestine
22	chr4:87950000-87955800	Enhancers	Fetal Intestine Small	intestine
23	chr4:87950000-87958600	Enhancers	Psoas Muscle	Psoas
24	chr4:87950000-87960200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:87950200-87955800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:87950200-87962600	Enhancers	Fetal Muscle Leg	muscle
27	chr4:87950400-87955400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:87950400-87955600	Enhancers	Fetal Kidney	kidney
29	chr4:87950600-87952600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:87950600-87952800	Enhancers	HSMMtube	muscle
31	chr4:87950600-87953200	Enhancers	Colonic Mucosa	Colon
32	chr4:87950600-87953400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr4:87950600-87955600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:87951000-87952800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr4:87951000-87953200	Enhancers	Placenta	Placenta
36	chr4:87951000-87953400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:87951000-87957800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr4:87951200-87953200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:87951200-87953400	Enhancers	Primary T cells from cord blood	blood
40	chr4:87951200-87953400	Enhancers	Primary hematopoietic stem cells	blood
41	chr4:87951200-87956000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:87951200-87956400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:87951400-87952600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:87951400-87952600	Enhancers	Fetal Brain Male	brain
45	chr4:87951400-87953000	Enhancers	GM12878-XiMat	blood
46	chr4:87951600-87953000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr4:87951600-87954400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr4:87951600-87955200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr4:87951600-87956400	Enhancers	Stomach Mucosa	stomach
50	chr4:87951600-87959000	Enhancers	Fetal Intestine Large	intestine

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