Variant report

Variant	rs10864000
Chromosome Location	chr1:212993414-212993415
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	FOXM1	chr1:212992969-212993515	GM12878	blood:	n/a	n/a
2	STAT3	chr1:212993238-212993526	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:212993095-212993584	GM12878	blood:	n/a	n/a
4	NFIC	chr1:212992868-212993685	GM12878	blood:	n/a	n/a
5	IKZF1	chr1:212993042-212993447	GM12878	blood:	n/a	n/a
6	TCF7L2	chr1:212993212-212993578	HepG2	liver:	n/a	chr1:212993270-212993279
7	MEF2A	chr1:212993013-212993542	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr1:212993004-212993507	GM12878	blood:	n/a	n/a
9	ELK1	chr1:212993078-212993535	GM12878	blood:	n/a	n/a
10	RELA	chr1:212993005-212993515	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212986725..212988338-chr1:212992887..212995652,2	K562	blood:
2	chr1:212969236..212971127-chr1:212991811..212994407,2	K562	blood:

Variant related genes	Relation type
ENSG00000236905	TF binding region
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10494955	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1054733	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863990	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863993	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863995	0.81[ASN][1000 genomes]
rs10863998	0.89[ASN][1000 genomes]
rs10863999	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120011	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120012	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120013	0.86[ASN][1000 genomes]
rs11120019	0.85[ASN][1000 genomes]
rs11120024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120025	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11120026	0.88[ASN][1000 genomes]
rs11120027	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11120032	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120037	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120039	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133462	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064985	0.86[ASN][1000 genomes]
rs12088916	0.88[ASN][1000 genomes]
rs12095846	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097897	0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12125321	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126017	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130945	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132316	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12136046	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12136834	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565557	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12722742	0.88[ASN][1000 genomes]
rs12734406	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12734543	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12737398	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741704	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743402	0.83[ASN][1000 genomes]
rs12744602	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12747251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2359322	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862953	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951463	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951638	0.86[ASN][1000 genomes]
rs6540761	0.84[EUR][1000 genomes]
rs6540763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6661720	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669492	0.80[ASN][1000 genomes]
rs6679350	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689604	0.95[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs6690689	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6693311	0.88[ASN][1000 genomes]
rs6694452	0.81[ASN][1000 genomes]
rs6697507	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700410	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702025	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6702611	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554105	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556272	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10864000	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs10864000	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
2	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
9	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:212988800-212993800	Weak transcription	Fetal Thymus	thymus
11	chr1:212990400-212995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:212990800-212998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:212991000-212998800	Weak transcription	Stomach Mucosa	stomach
14	chr1:212992400-212993600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:212992400-212994000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:212992400-212994600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:212992400-212994800	Enhancers	HepG2	liver
18	chr1:212992600-212993600	Enhancers	Fetal Intestine Large	intestine
19	chr1:212992600-212993600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr1:212992600-212994000	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:212992800-212993600	Flanking Active TSS	GM12878-XiMat	blood
22	chr1:212992800-212993800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:212993000-212993600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:212993200-212994000	Enhancers	Primary B cells from cord blood	blood
25	chr1:212993200-212995000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:212993400-212994200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:212993400-212994400	Enhancers	Primary hematopoietic stem cells	blood

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