Variant report

Variant	rs35949820
Chromosome Location	chr9:137004530-137004531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:137003273-137004552	HepG2	liver:	n/a	n/a
2	FOXP2	chr9:137004255-137004558	SK-N-MC	brain:	n/a	n/a
3	CEBPB	chr9:137004186-137004677	IMR90	lung:	n/a	chr9:137004481-137004492
4	CEBPB	chr9:137004215-137004596	MCF-7	breast:	n/a	chr9:137004481-137004492
5	CEBPB	chr9:137004298-137004653	A549	lung:	n/a	chr9:137004481-137004492
6	CEBPB	chr9:137004309-137004683	K562	blood:	n/a	chr9:137004481-137004492
7	POLR2A	chr9:137004334-137004559	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr9:137004292-137004591	A549	lung:	n/a	chr9:137004481-137004492
9	CEBPB	chr9:137004341-137004621	K562	blood:	n/a	chr9:137004481-137004492
10	CEBPB	chr9:137004174-137004781	A549	lung:	n/a	chr9:137004481-137004492
11	CEBPB	chr9:137004287-137004670	HepG2	liver:	n/a	chr9:137004481-137004492
12	CTCF	chr9:137004520-137004670	NHLF	lung:	n/a	n/a
13	CEBPB	chr9:137004310-137004668	Hela-S3	cervix:	n/a	chr9:137004481-137004492
14	CEBPB	chr9:137004356-137004643	H1-hESC	embryonic stem cell:	n/a	chr9:137004481-137004492

No.	Distal block	Cell Line	Cell type
1	chr9:136932690..136935080-chr9:137003441..137005032,2	MCF-7	breast:
2	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
3	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000273249	TF binding region
ENSG00000169925	Chromatin interaction
ENSG00000221676	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1128044	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11556390	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28410119	0.83[ASN][1000 genomes]
rs28412218	0.94[ASN][1000 genomes]
rs28415637	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28428662	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28438574	0.98[ASN][1000 genomes]
rs28464304	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs28473092	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28475221	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485659	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28490920	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28498266	0.89[ASW][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs28508246	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522840	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28549758	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28567437	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28588875	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28604373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28610236	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28611335	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28635910	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28637447	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28647893	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28648812	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28661406	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28681320	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28681533	0.86[AFR][1000 genomes]
rs28695913	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28705801	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34417824	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35401074	0.85[ASN][1000 genomes]
rs35715743	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36185416	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4358859	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4744560	0.81[CEU][hapmap];0.92[GIH][hapmap];0.80[EUR][1000 genomes]
rs55874211	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7847227	0.81[EUR][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	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active 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	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137001600-137004600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:137002000-137004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:137002400-137004600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr9:137002400-137004600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:137002400-137004600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr9:137002400-137004600	Enhancers	Esophagus	oesophagus
7	chr9:137002400-137004600	Enhancers	Ovary	ovary
8	chr9:137002400-137004600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr9:137002400-137004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:137002400-137004800	Enhancers	Adipose Nuclei	Adipose
11	chr9:137002400-137004800	Enhancers	Left Ventricle	heart
12	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:137002600-137004600	Enhancers	Brain Substantia Nigra	brain
16	chr9:137002600-137004800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:137002600-137005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:137002600-137005000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:137002600-137005000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:137002600-137005000	Enhancers	Pancreas	Pancrea
21	chr9:137002600-137005200	Genic enhancers	Fetal Intestine Small	intestine
22	chr9:137002600-137005800	Genic enhancers	Fetal Stomach	stomach
23	chr9:137002800-137004600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr9:137002800-137004800	Enhancers	Colon Smooth Muscle	Colon
25	chr9:137003000-137004600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:137003000-137004600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr9:137003000-137004600	Enhancers	Right Atrium	heart
28	chr9:137003000-137005200	Weak transcription	K562	blood
29	chr9:137003200-137004600	Enhancers	Liver	Liver
30	chr9:137003200-137004600	Flanking Active TSS	Fetal Brain Female	brain
31	chr9:137003200-137004600	Enhancers	Psoas Muscle	Psoas
32	chr9:137003200-137004600	Transcr. at gene 5' and 3'	Hela-S3	cervix
33	chr9:137003200-137004800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:137003200-137004800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr9:137003200-137005600	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr9:137003200-137005800	Genic enhancers	Fetal Muscle Leg	muscle
37	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:137003400-137004600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr9:137003400-137004600	Genic enhancers	Spleen	Spleen
40	chr9:137003400-137004600	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr9:137003400-137004600	Flanking Active TSS	NHDF-Ad	bronchial
42	chr9:137003600-137004600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:137003600-137004600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:137003600-137004600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:137003600-137004600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:137003600-137004600	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr9:137003600-137004600	Genic enhancers	HMEC	breast
48	chr9:137003600-137004800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:137003600-137005200	Weak transcription	Primary B cells from cord blood	blood
50	chr9:137003600-137007600	Weak transcription	Primary hematopoietic stem cells	blood

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