Variant report

Variant	rs4743277
Chromosome Location	chr9:101557529-101557530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr9:101557513-101557531	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101555483..101562112-chr9:101568669..101573087,9	K562	blood:
2	chr9:101534630..101537208-chr9:101556445..101558370,2	MCF-7	breast:
3	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
4	chr9:101546085..101548581-chr9:101557389..101560839,3	MCF-7	breast:
5	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:

No data

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000165138	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10119228	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10125255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739704	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10987230	1.00[CEU][hapmap]
rs10987234	1.00[CEU][hapmap]
rs10987293	1.00[CEU][hapmap]
rs10987843	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1167771	1.00[CEU][hapmap]
rs1555520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs180038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180039	0.91[ASN][1000 genomes]
rs182877	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1930130	1.00[CEU][hapmap]
rs2058881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2778916	1.00[CEU][hapmap]
rs2778919	1.00[CEU][hapmap]
rs2779539	1.00[CEU][hapmap]
rs337527	1.00[CEU][hapmap]
rs337564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337566	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337567	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337568	0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs337583	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337589	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs337590	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371521	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4133240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4133831	0.87[EUR][1000 genomes]
rs429562	0.87[EUR][1000 genomes]
rs439347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs453409	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742740	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743279	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4743280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743283	0.82[EUR][1000 genomes]
rs48418	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507318	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6415847	0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6415849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7846846	0.91[ASN][1000 genomes]
rs7861840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409306	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967932	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4743277	CRX	trans	brain	seeQTL
rs4743277	GSG1	trans	brain	seeQTL
rs4743277	LRTM1	trans	brain	seeQTL
rs4743277	SLC5A7	trans	brain	seeQTL
rs4743277	CD247	trans	brain	seeQTL
rs4743277	DEFB119	trans	brain	seeQTL
rs4743277	GUCA1C	trans	brain	seeQTL
rs4743277	SH2D2A	trans	brain	seeQTL
rs4743277	ASMT	trans	brain	seeQTL
rs4743277	TTR	trans	brain	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
2	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
4	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
5	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
6	chr9:101544200-101557600	Weak transcription	Colonic Mucosa	Colon
7	chr9:101544800-101557600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:101546200-101557600	Weak transcription	Left Ventricle	heart
9	chr9:101552600-101557600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:101552600-101557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:101552800-101557600	Weak transcription	Aorta	Aorta
12	chr9:101553200-101558000	Weak transcription	Thymus	Thymus
13	chr9:101553600-101557600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:101553600-101557800	Weak transcription	GM12878-XiMat	blood
15	chr9:101554000-101557600	Weak transcription	NH-A	brain
16	chr9:101554200-101557800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:101554400-101557600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:101554400-101557600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:101554600-101557600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:101554600-101557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:101554600-101557600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:101554600-101557600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:101554600-101557600	Weak transcription	Ovary	ovary
24	chr9:101554600-101557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:101554600-101557600	Weak transcription	A549	lung
26	chr9:101554600-101557800	Weak transcription	Placenta	Placenta
27	chr9:101554600-101558000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:101554800-101557600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:101554800-101557600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr9:101554800-101557600	Weak transcription	HSMM	muscle
31	chr9:101555600-101557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:101555600-101557600	Weak transcription	HMEC	breast
33	chr9:101556200-101557600	Enhancers	Lung	lung
34	chr9:101556400-101557800	Enhancers	Gastric	stomach
35	chr9:101556600-101557600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:101556600-101557600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:101556600-101557600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:101556600-101557600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:101556600-101557600	Enhancers	Colon Smooth Muscle	Colon
40	chr9:101556600-101557600	Enhancers	Fetal Muscle Leg	muscle
41	chr9:101556600-101557800	Enhancers	Brain Anterior Caudate	brain
42	chr9:101556600-101557800	Enhancers	Fetal Stomach	stomach
43	chr9:101556600-101557800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr9:101556800-101557600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:101556800-101557600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr9:101556800-101557800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:101556800-101559400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr9:101557000-101557600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr9:101557000-101557600	Enhancers	Dnd41	blood
50	chr9:101557000-101557800	Enhancers	Primary T cells from cord blood	blood

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