Variant report

Variant	rs340652
Chromosome Location	chr4:87935730-87935731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87854648..87860283-chr4:87935219..87941983,10	K562	blood:
2	chr4:87854102..87856628-chr4:87934651..87937317,2	MCF-7	breast:
3	chr4:87934960..87936958-chr4:87949259..87951055,2	MCF-7	breast:
4	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

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

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10022960	0.92[ASN][1000 genomes]
rs11931688	1.00[CEU][hapmap]
rs11933302	1.00[CEU][hapmap]
rs1374936	0.83[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs168161	1.00[ASN][1000 genomes]
rs17012279	1.00[CEU][hapmap]
rs17012291	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2053774	0.91[ASN][1000 genomes]
rs2272777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.83[ASN][1000 genomes]
rs340627	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340628	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340629	0.97[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs340632	0.96[ASN][1000 genomes]
rs340635	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340640	0.97[ASN][1000 genomes]
rs340644	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.97[ASN][1000 genomes]
rs340645	0.97[ASN][1000 genomes]
rs340646	0.92[ASN][1000 genomes]
rs340647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs4536897	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4693155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4693799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs58317309	0.93[ASN][1000 genomes]
rs6531943	0.97[ASN][1000 genomes]
rs6531944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs6531947	0.97[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6822432	1.00[CEU][hapmap]
rs6824639	1.00[CEU][hapmap]
rs6848056	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6853011	0.92[ASN][1000 genomes]
rs6855627	1.00[CEU][hapmap]
rs73837575	0.97[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs895740	0.83[ASN][1000 genomes]
rs965824	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340652	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87929200-87939400	Weak transcription	Gastric	stomach
2	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
3	chr4:87929600-87937000	Enhancers	Fetal Heart	heart
4	chr4:87929600-87938000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:87929600-87938800	Weak transcription	HSMMtube	muscle
6	chr4:87929800-87936600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:87929800-87937000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:87930600-87937000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:87930600-87940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
12	chr4:87930800-87940600	Weak transcription	Spleen	Spleen
13	chr4:87931000-87936800	Enhancers	Primary T cells from cord blood	blood
14	chr4:87931000-87936800	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:87931000-87937200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:87931000-87940800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr4:87931000-87940800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:87931000-87946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:87931200-87937200	Enhancers	Colon Smooth Muscle	Colon
20	chr4:87931200-87940400	Enhancers	Primary B cells from cord blood	blood
21	chr4:87931200-87943400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:87931800-87942600	Enhancers	Primary hematopoietic stem cells	blood
23	chr4:87932400-87936800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr4:87932600-87935800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:87932600-87937000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:87932600-87937000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:87932600-87938200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:87932600-87938800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:87932800-87936800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr4:87932800-87936800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr4:87933200-87937000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr4:87933200-87937000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:87933200-87937000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:87933200-87937200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:87933200-87938800	Weak transcription	Brain Substantia Nigra	brain
36	chr4:87933200-87938800	Weak transcription	NH-A	brain
37	chr4:87933200-87941000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:87933400-87937000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr4:87933400-87937400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:87933800-87938800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:87934000-87935800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr4:87934000-87936000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:87934200-87936000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:87934200-87937400	Enhancers	HepG2	liver
45	chr4:87934200-87939200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:87934200-87939200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:87934400-87936400	Flanking Active TSS	GM12878-XiMat	blood
48	chr4:87934400-87937000	Flanking Active TSS	A549	lung
49	chr4:87934400-87938000	Enhancers	Fetal Intestine Large	intestine
50	chr4:87934400-87940800	Enhancers	Fetal Intestine Small	intestine

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