Variant report

Variant	rs10753688
Chromosome Location	chr1:165666448-165666449
allele	C/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	IRF1	chr1:165665543-165666651	K562	blood:	n/a	chr1:165665640-165665653 chr1:165665818-165665835 chr1:165666348-165666360 chr1:165665642-165665656 chr1:165665641-165665658
2	E2F4	chr1:165665922-165668273	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:165665838-165666835	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFF	chr1:165665407-165666588	K562	blood:	n/a	chr1:165665947-165665965 chr1:165665946-165665960
5	MAFK	chr1:165665230-165666511	IMR90	lung:	n/a	chr1:165665945-165665961 chr1:165665948-165665963 chr1:165666007-165666021 chr1:165665943-165665963 chr1:165665946-165665960
6	MAFK	chr1:165665553-165666818	K562	blood:	n/a	chr1:165665945-165665961 chr1:165665948-165665963 chr1:165666007-165666021 chr1:165665943-165665963 chr1:165665946-165665960
7	GATA3	chr1:165666329-165666505	SH-SY5Y	brain:	n/a	chr1:165666375-165666382 chr1:165666368-165666389 chr1:165666375-165666384 chr1:165666374-165666384
8	RFX5	chr1:165666399-165666721	K562	blood:	n/a	n/a
9	POLR2A	chr1:165666214-165666642	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:165599643..165601355-chr1:165666069..165669053,3	MCF-7	breast:
2	chr1:165664693..165666961-chr1:165728750..165730425,2	K562	blood:
3	chr1:165599737..165602284-chr1:165666440..165669733,4	K562	blood:
4	chr1:165666145..165668955-chr1:165675306..165678474,3	K562	blood:
5	chr1:165666281..165669188-chr1:165795955..165797975,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215838	TF binding region
ENSG00000143179	Chromatin interaction
ENSG00000273365	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000215838	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10753689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800131	0.81[CEU][hapmap]
rs10800132	0.93[ASN][1000 genomes]
rs10800133	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10918241	0.84[TSI][hapmap]
rs10918242	0.90[ASN][1000 genomes]
rs10918245	0.86[ASN][1000 genomes]
rs10918251	0.93[ASN][1000 genomes]
rs10918252	0.93[ASN][1000 genomes]
rs1143659	0.82[TSI][hapmap]
rs12021795	0.81[ASN][1000 genomes]
rs12033254	0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12036561	0.90[ASN][1000 genomes]
rs12037790	0.92[ASN][1000 genomes]
rs12084748	0.93[ASN][1000 genomes]
rs12409168	0.92[ASN][1000 genomes]
rs12567331	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12728137	0.88[ASN][1000 genomes]
rs1337442	0.82[TSI][hapmap]
rs1538115	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs17482717	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1913844	0.82[TSI][hapmap]
rs4307543	0.90[ASN][1000 genomes]
rs4576644	0.84[ASN][1000 genomes]
rs4578194	0.81[CHD][hapmap]
rs4646883	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4646885	0.92[ASN][1000 genomes]
rs4646886	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs4657463	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4657466	0.93[ASN][1000 genomes]
rs4657468	0.80[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs71628390	0.93[ASN][1000 genomes]
rs7541817	0.90[ASN][1000 genomes]
rs7546215	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7546322	0.93[ASN][1000 genomes]
rs7555787	0.82[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10753688	ALDH9A1	cis	Esophagus Mucosa	GTEx
rs10753688	Y_RNA	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:165650000-165666800	Weak transcription	Colonic Mucosa	Colon
3	chr1:165651600-165667200	Weak transcription	Gastric	stomach
4	chr1:165652200-165666800	Weak transcription	Lung	lung
5	chr1:165652400-165666800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:165652400-165666800	Weak transcription	Esophagus	oesophagus
7	chr1:165652400-165667000	Weak transcription	Pancreas	Pancrea
8	chr1:165652400-165667000	Weak transcription	Spleen	Spleen
9	chr1:165655600-165666800	Weak transcription	Aorta	Aorta
10	chr1:165655600-165666800	Weak transcription	Right Ventricle	heart
11	chr1:165656000-165666800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:165660200-165666800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:165660200-165666800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:165660400-165666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:165660400-165667000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:165663600-165666800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:165664200-165666800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:165664400-165666800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:165664600-165666600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:165665000-165666800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:165665200-165666800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:165665200-165667000	Flanking Active TSS	Liver	Liver
23	chr1:165665200-165667200	Enhancers	Fetal Heart	heart
24	chr1:165665400-165666600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:165665400-165666600	Flanking Active TSS	Hela-S3	cervix
26	chr1:165665400-165666600	Flanking Active TSS	HMEC	breast
27	chr1:165665400-165666600	Flanking Active TSS	NH-A	brain
28	chr1:165665400-165666600	Flanking Active TSS	NHDF-Ad	bronchial
29	chr1:165665400-165666800	Enhancers	Primary B cells from cord blood	blood
30	chr1:165665400-165666800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:165665400-165666800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:165665400-165666800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:165665400-165666800	Enhancers	Colon Smooth Muscle	Colon
34	chr1:165665400-165666800	Enhancers	Stomach Mucosa	stomach
35	chr1:165665400-165667000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:165665400-165667000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:165665400-165667000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:165665400-165667000	Flanking Active TSS	Osteobl	bone
39	chr1:165665400-165667200	Flanking Active TSS	HUVEC	blood vessel
40	chr1:165665400-165668400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:165665400-165668400	Active TSS	NHLF	lung
42	chr1:165665600-165666600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr1:165665600-165666600	Flanking Active TSS	NHEK	skin
44	chr1:165665600-165666800	Enhancers	HepG2	liver
45	chr1:165665600-165667000	Flanking Active TSS	Dnd41	blood
46	chr1:165665600-165667600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:165665800-165666600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr1:165665800-165666600	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:165665800-165666800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr1:165665800-165666800	Enhancers	Primary B cells from peripheral blood	blood

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