Variant report

Variant	rs1638736
Chromosome Location	chr7:66092308-66092309
allele	A/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	SPI1	chr7:66092255-66092614	GM12878	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
2	STAT3	chr7:66092269-66092716	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr7:66091656-66092336	HepG2	liver:	n/a	n/a
4	CREB1	chr7:66092038-66092551	HepG2	liver:	n/a	n/a
5	ZNF143	chr7:66092260-66092371	GM12878	blood:	n/a	n/a
6	SPI1	chr7:66092205-66092650	HL-60	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
7	GATA2	chr7:66091819-66092663	SH-SY5Y	brain:	n/a	n/a
8	CEBPB	chr7:66091533-66092524	IMR90	lung:	n/a	chr7:66091783-66091794
9	EP300	chr7:66091491-66096076	SK-N-SH	brain:	n/a	chr7:66093761-66093770 chr7:66094701-66094715 chr7:66093402-66093418 chr7:66094696-66094710 chr7:66093421-66093437
10	RCOR1	chr7:66092208-66092515	HepG2	liver:	n/a	n/a
11	EP300	chr7:66091969-66092502	SK-N-SH_RA	brain:	n/a	n/a
12	TCF7L2	chr7:66091878-66092540	HEK293	kidney:	n/a	n/a
13	POLR2A	chr7:66092091-66092585	SK-N-SH	brain:	n/a	n/a
14	SPI1	chr7:66092290-66092570	GM12878	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
15	RAD21	chr7:66092204-66092575	SK-N-SH_RA	brain:	n/a	n/a
16	EP300	chr7:66092092-66092466	SK-N-SH_RA	brain:	n/a	n/a
17	TBP	chr7:66091734-66092509	HepG2	liver:	n/a	n/a
18	EBF1	chr7:66092238-66092481	GM12878	blood:	n/a	chr7:66092325-66092336
19	MYC	chr7:66092241-66092727	NB4	blood:	n/a	n/a
20	JUND	chr7:66092101-66092417	HepG2	liver:	n/a	n/a
21	EP300	chr7:66092248-66092628	GM12878	blood:	n/a	n/a
22	SPI1	chr7:66092301-66092621	GM12891	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
23	FOXA2	chr7:66092202-66092390	HepG2	liver:	n/a	n/a
24	MAX	chr7:66092102-66092730	NB4	blood:	n/a	n/a
25	SPI1	chr7:66092287-66092619	GM12891	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
26	CREB1	chr7:66092116-66092661	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:66091849-66094789	IMR90	lung:	n/a	n/a
28	MXI1	chr7:66091233-66095157	SK-N-SH	brain:	n/a	n/a
29	SPI1	chr7:66092170-66092630	HL-60	blood:	n/a	chr7:66092409-66092416 chr7:66092505-66092514
30	GATA3	chr7:66091909-66092577	SH-SY5Y	brain:	n/a	n/a
31	POLR2A	chr7:66092116-66092598	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66054686..66058308-chr7:66092199..66095155,8	MCF-7	breast:
2	chr7:66065925..66067738-chr7:66091765..66093864,2	MCF-7	breast:
3	chr7:66091898..66097382-chr7:66117985..66122507,10	K562	blood:
4	chr7:66091926..66093448-chr7:66145464..66148372,2	K562	blood:
5	chr7:66081713..66084655-chr7:66091720..66093835,2	K562	blood:
6	chr7:66091844..66094640-chr7:66118336..66122170,5	MCF-7	breast:
7	chr7:66091921..66093533-chr7:66126836..66128952,2	K562	blood:

Variant related genes	Relation type
KCTD7	TF binding region
ENSG00000226824	Chromatin interaction
ENSG00000232559	Chromatin interaction
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1267816	0.90[ASN][1000 genomes]
rs1267817	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1267818	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1267819	0.90[ASN][1000 genomes]
rs1267820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12698542	0.88[ASN][1000 genomes]
rs13222887	0.81[ASN][1000 genomes]
rs13224048	0.83[ASN][1000 genomes]
rs13232193	1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13236129	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13237037	0.83[ASN][1000 genomes]
rs13237344	0.86[ASN][1000 genomes]
rs13242216	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13247442	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1573944	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1618893	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1622330	0.86[EUR][1000 genomes]
rs1638731	0.93[ASN][1000 genomes]
rs1638734	1.00[ASN][1000 genomes]
rs1796215	0.93[ASN][1000 genomes]
rs1796220	0.90[ASN][1000 genomes]
rs1796228	0.90[ASN][1000 genomes]
rs1796229	0.88[ASN][1000 genomes]
rs1882655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1922723	0.89[ASN][1000 genomes]
rs1962049	0.87[CEU][hapmap]
rs2141924	0.88[ASN][1000 genomes]
rs2178742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2420609	0.82[ASN][1000 genomes]
rs2533287	0.96[ASN][1000 genomes]
rs2533288	0.90[ASN][1000 genomes]
rs2659903	0.88[ASN][1000 genomes]
rs2659911	0.95[ASN][1000 genomes]
rs2659913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2707823	0.86[ASN][1000 genomes]
rs2707826	0.90[ASN][1000 genomes]
rs2707828	0.90[ASN][1000 genomes]
rs2707830	0.93[ASN][1000 genomes]
rs2707831	0.93[ASN][1000 genomes]
rs2707832	0.95[ASN][1000 genomes]
rs2707833	0.95[ASN][1000 genomes]
rs2707838	0.95[ASN][1000 genomes]
rs2707840	0.95[ASN][1000 genomes]
rs2707844	0.88[ASN][1000 genomes]
rs34073431	0.82[ASN][1000 genomes]
rs35261784	0.83[ASN][1000 genomes]
rs35370033	1.00[ASN][1000 genomes]
rs35825036	0.83[ASN][1000 genomes]
rs3800822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3936	0.95[ASN][1000 genomes]
rs58668827	0.83[ASN][1000 genomes]
rs60326618	0.93[ASN][1000 genomes]
rs6460312	0.95[ASN][1000 genomes]
rs66510832	0.88[EUR][1000 genomes]
rs66630579	0.93[ASN][1000 genomes]
rs71563118	0.81[ASN][1000 genomes]
rs73135918	0.91[ASN][1000 genomes]
rs73150635	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1638736	ASL	cis	multi-tissue	Pritchard
rs1638736	GUSB	cis	Whole Blood	GTEx
rs1638736	VKORC1L1	cis	Whole Blood	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66086800-66092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66087600-66092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:66089800-66092800	Enhancers	Placenta	Placenta
4	chr7:66090200-66092800	Weak transcription	Stomach Mucosa	stomach
5	chr7:66090400-66092800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:66090600-66093000	Enhancers	NHLF	lung
7	chr7:66090800-66092800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:66091200-66092400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr7:66091400-66092400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:66091400-66092400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:66091400-66092800	Enhancers	Osteobl	bone
12	chr7:66091400-66093000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:66091600-66092400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:66091600-66092800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:66091800-66092600	Flanking Active TSS	HepG2	liver
16	chr7:66091800-66092600	Enhancers	NHEK	skin
17	chr7:66091800-66092800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:66091800-66092800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:66091800-66092800	Enhancers	Fetal Stomach	stomach
20	chr7:66091800-66093000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:66092000-66092400	Enhancers	Primary B cells from cord blood	blood
22	chr7:66092000-66092400	Active TSS	Stomach Smooth Muscle	stomach
23	chr7:66092000-66092600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:66092000-66092800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:66092000-66092800	Enhancers	Hela-S3	cervix
26	chr7:66092000-66094400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr7:66092200-66092400	Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr7:66092200-66092600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:66092200-66092600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr7:66092200-66092600	Flanking Active TSS	GM12878-XiMat	blood
31	chr7:66092200-66092600	Flanking Active TSS	NHDF-Ad	bronchial
32	chr7:66092200-66092800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr7:66092200-66092800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:66092200-66092800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:66092200-66092800	Enhancers	Adipose Nuclei	Adipose
36	chr7:66092200-66092800	Enhancers	Brain Cingulate Gyrus	brain
37	chr7:66092200-66092800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr7:66092200-66092800	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:66092200-66092800	Enhancers	Duodenum Mucosa	Duodenum
40	chr7:66092200-66092800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr7:66092200-66092800	Enhancers	Pancreas	Pancrea
42	chr7:66092200-66092800	Enhancers	K562	blood
43	chr7:66092200-66092800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr7:66092200-66093200	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr7:66092200-66094600	Active TSS	Brain Anterior Caudate	brain
46	chr7:66092200-66094800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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