Variant report

Variant	rs447990
Chromosome Location	chr4:88033352-88033353
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	chr4:88033021-88033487	HepG2	liver:	n/a	n/a
2	BHLHE40	chr4:88033233-88033667	K562	blood:	n/a	n/a
3	EP300	chr4:88033349-88033706	K562	blood:	n/a	chr4:88033584-88033598 chr4:88033596-88033605
4	POLR2A	chr4:88032758-88033779	GM12878	blood:	n/a	n/a
5	NFYA	chr4:88033289-88033417	GM12878	blood:	n/a	n/a
6	CCNT2	chr4:88033192-88033691	K562	blood:	n/a	n/a
7	CEBPB	chr4:88033260-88033516	K562	blood:	n/a	n/a
8	MAFK	chr4:88033291-88033564	K562	blood:	n/a	n/a
9	JUND	chr4:88033172-88033705	K562	blood:	n/a	chr4:88033510-88033517 chr4:88033264-88033273
10	GATA1	chr4:88032918-88033833	PBDE	blood:	n/a	chr4:88033592-88033603
11	CUX1	chr4:88033179-88033948	K562	blood:	n/a	n/a
12	MYC	chr4:88033301-88033458	K562	blood:	n/a	n/a
13	POLR2A	chr4:88033098-88033798	K562	blood:	n/a	n/a
14	HMGN3	chr4:88033211-88033663	K562	blood:	n/a	n/a
15	ARID3A	chr4:88033310-88033619	K562	blood:	n/a	n/a
16	RCOR1	chr4:88033204-88033694	K562	blood:	n/a	n/a
17	CREB1	chr4:88033261-88033893	K562	blood:	n/a	n/a
18	ATF1	chr4:88033199-88033731	K562	blood:	n/a	n/a
19	TAL1	chr4:88033335-88033728	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88030647..88032451-chr4:88032787..88035472,2	MCF-7	breast:
2	chr4:88032951..88035880-chr4:88037819..88039540,2	MCF-7	breast:
3	chr4:87927502..87929232-chr4:88032262..88034654,2	MCF-7	breast:
4	chr4:88033201..88035893-chr4:88037501..88039381,2	K562	blood:

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10018897	0.88[ASN][1000 genomes]
rs1037814	0.87[LWK][hapmap]
rs10516789	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs168204	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs19026	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2125787	0.82[MKK][hapmap]
rs236674	0.96[ASN][1000 genomes]
rs236675	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs236678	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs236685	0.96[ASN][1000 genomes]
rs236686	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs236687	0.96[ASN][1000 genomes]
rs236996	0.81[MKK][hapmap]
rs2869642	0.94[ASN][1000 genomes]
rs2926512	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3116679	0.96[ASN][1000 genomes]
rs342436	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs342438	0.80[LWK][hapmap]
rs342457	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs342458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342460	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs342461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342462	0.93[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs342465	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs342467	0.85[LWK][hapmap]
rs3775225	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3822042	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs384059	0.86[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs390604	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs393991	0.88[ASN][1000 genomes]
rs411365	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs442177	0.83[YRI][hapmap]
rs60757751	0.98[ASN][1000 genomes]
rs6827213	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9992235	0.88[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	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
2	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
3	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
4	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
5	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
6	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3361742	chr4:88031428-88033676	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs447990	TIGD2	cis	cerebellum	SCAN
rs447990	HSD17B13	cis	parietal	SCAN
rs447990	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:88015800-88035400	Weak transcription	Right Ventricle	heart
3	chr4:88018600-88034200	Weak transcription	Fetal Stomach	stomach
4	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:88021000-88034200	Weak transcription	Spleen	Spleen
6	chr4:88021600-88036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:88021600-88037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:88021800-88036000	Weak transcription	Brain Angular Gyrus	brain
9	chr4:88025600-88034200	Weak transcription	Lung	lung
10	chr4:88025600-88035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:88025600-88035800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:88026200-88042200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:88026400-88042400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:88026600-88033600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:88026600-88042200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:88026600-88042600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:88026800-88035800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:88027000-88035400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:88027000-88037600	Strong transcription	Liver	Liver
22	chr4:88028400-88035800	Weak transcription	Psoas Muscle	Psoas
23	chr4:88029200-88035400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:88029400-88034200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:88029600-88034200	Weak transcription	Esophagus	oesophagus
26	chr4:88029600-88034200	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:88029600-88034200	Weak transcription	Gastric	stomach
28	chr4:88029600-88034400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:88029600-88035400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:88029600-88035800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:88029600-88035800	Weak transcription	Aorta	Aorta
32	chr4:88029600-88035800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:88029600-88035800	Weak transcription	Pancreas	Pancrea
34	chr4:88029600-88035800	Weak transcription	Right Atrium	heart
35	chr4:88029600-88036000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:88029600-88036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:88029800-88035800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:88029800-88037400	Weak transcription	Fetal Heart	heart
39	chr4:88029800-88041600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:88030000-88048800	Weak transcription	A549	lung
41	chr4:88030200-88034800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:88030200-88036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:88030200-88036000	Weak transcription	Osteobl	bone
44	chr4:88030200-88036200	Weak transcription	Small Intestine	intestine
45	chr4:88030400-88035800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:88030400-88035800	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:88030400-88036000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:88030600-88034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:88030600-88034200	Weak transcription	Fetal Intestine Small	intestine
50	chr4:88030600-88035800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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