Variant report

Variant	rs1460961
Chromosome Location	chr5:60411832-60411833
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	SPI1	chr5:60411771-60412135	GM12891	blood:	n/a	n/a
2	RUNX3	chr5:60411818-60412171	GM12878	blood:	n/a	n/a
3	SPI1	chr5:60411653-60412129	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000269267	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1021005	0.81[EUR][1000 genomes]
rs10805374	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10939879	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10939881	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939882	0.84[AFR][1000 genomes]
rs11739952	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516995	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12517310	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518404	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12518792	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12652830	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12653132	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12655209	0.87[EUR][1000 genomes]
rs12655603	0.81[EUR][1000 genomes]
rs1382917	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471488	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1479645	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1526896	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159535	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159536	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs159537	0.88[YRI][hapmap]
rs17419290	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17444495	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1983484	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049579	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2120956	0.81[EUR][1000 genomes]
rs2120957	0.81[EUR][1000 genomes]
rs28436304	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2898309	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34608	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34609	0.91[LWK][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs34616	0.81[LWK][hapmap]
rs34617	0.87[YRI][hapmap]
rs34619	0.96[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797559	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4642318	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647052	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647132	0.80[EUR][1000 genomes]
rs4699969	0.84[AFR][1000 genomes]
rs4700402	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4700404	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4700407	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55738840	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55814394	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56025209	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56031340	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56284222	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56350217	0.85[EUR][1000 genomes]
rs58646987	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60858663	0.81[EUR][1000 genomes]
rs61017995	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61101592	0.81[EUR][1000 genomes]
rs62365455	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62365458	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62367862	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62367872	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62367878	0.83[EUR][1000 genomes]
rs62367879	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62367885	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62367903	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62372133	0.81[EUR][1000 genomes]
rs62372134	0.81[EUR][1000 genomes]
rs6449512	0.84[EUR][1000 genomes]
rs67490467	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68104763	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6884966	0.81[EUR][1000 genomes]
rs726824	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72757187	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72759206	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72759215	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706753	0.82[AFR][1000 genomes]
rs7709522	0.88[EUR][1000 genomes]
rs7713481	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7714396	0.88[EUR][1000 genomes]
rs7722373	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7723349	0.83[ASN][1000 genomes]
rs7723901	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7734205	0.89[EUR][1000 genomes]
rs7737276	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868791	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs888799	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9687099	0.81[EUR][1000 genomes]
rs976630	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs976631	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1460961	DEPDC1B	cis	cerebellum	SCAN
rs1460961	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs1460961	mimitin	cis	multi-tissue	Pritchard
rs1460961	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs1460961	KIF2A	cis	parietal	SCAN
rs1460961	ERCC8	cis	multi-tissue	Pritchard
rs1460961	ELOVL7	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60381000-60419400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:60394400-60415400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:60395400-60428200	Weak transcription	HSMMtube	muscle
4	chr5:60396800-60415400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:60396800-60420400	Weak transcription	Ovary	ovary
6	chr5:60398400-60416800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:60398400-60418800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:60402800-60420600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:60408200-60418600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:60409400-60412400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:60409600-60418600	Weak transcription	Fetal Intestine Small	intestine
13	chr5:60409800-60412000	Weak transcription	Fetal Stomach	stomach
14	chr5:60410400-60418800	Weak transcription	Gastric	stomach
15	chr5:60411200-60420600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:60411200-60422400	Weak transcription	Aorta	Aorta

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