Variant report

Variant	rs7485402
Chromosome Location	chr12:9864392-9864393
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9798330..9801052-chr12:9860989..9864813,3	K562	blood:

Variant related genes	Relation type
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10772060	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10844418	1.00[CHB][hapmap]
rs10844424	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs10844429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs11052430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs11052431	1.00[CHB][hapmap]
rs11052718	0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs12369995	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12370579	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12371503	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12371981	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12371982	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap]
rs12582616	0.83[ASN][1000 genomes]
rs12809752	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12810851	1.00[CHB][hapmap]
rs12812783	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12814560	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12816660	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12817550	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12817743	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12818179	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12819865	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12820674	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12823653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	1.00[CHB][hapmap]
rs12825507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12828602	1.00[CHB][hapmap]
rs12830448	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12830867	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12830878	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1861089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2080207	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114872	1.00[CHB][hapmap]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.83[ASN][1000 genomes]
rs34623781	0.89[ASN][1000 genomes]
rs34826829	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35078787	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35512621	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763280	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763813	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes]
rs4763814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.83[ASN][1000 genomes]
rs66725265	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67429242	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71441764	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7310897	1.00[CHB][hapmap]
rs7954062	0.89[ASN][1000 genomes]
rs7961812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7961903	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974554	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7975557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7975865	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	1.00[CHB][hapmap]
rs982511	1.00[CHD][hapmap];0.83[ASN][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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv442255	chr12:9862078-9874924	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3693109	chr12:9863968-9876091	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7485402	DCAL1	cis	multi-tissue	Pritchard
rs7485402	CLEC2D	cis	multi-tissue	Pritchard
rs7485402	ACTG2	trans	brain	seeQTL
rs7485402	GSG1	cis	parietal	SCAN
rs7485402	LOC171220	cis	cerebellum	SCAN
rs7485402	C12orf59	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:9858000-9872200	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:9859000-9870200	Enhancers	Primary B cells from cord blood	blood
4	chr12:9860800-9864400	Weak transcription	A549	lung
5	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
7	chr12:9861400-9864400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:9861400-9864600	Weak transcription	Primary T cells from cord blood	blood
9	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:9861800-9868200	Enhancers	GM12878-XiMat	blood
11	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:9863000-9864600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:9863200-9864800	Enhancers	HSMMtube	muscle
14	chr12:9863400-9864800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:9863400-9864800	Enhancers	Fetal Heart	heart
16	chr12:9863600-9864600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:9863800-9864600	Enhancers	HSMM	muscle
18	chr12:9863800-9864800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:9864000-9865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:9864200-9864600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:9864200-9864800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links