Variant report

Variant	rs12582616
Chromosome Location	chr12:9889616-9889617
allele	A/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	RFX5	chr12:9889587-9889666	GM12878	blood:	n/a	n/a
2	EP300	chr12:9889603-9889901	GM12878	blood:	n/a	chr12:9889781-9889790 chr12:9889757-9889766
3	SPI1	chr12:9889463-9889975	HL-60	blood:	n/a	chr12:9889755-9889768 chr12:9889778-9889791 chr12:9889754-9889767
4	KAP1	chr12:9889297-9889817	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9888502..9890048-chr12:9893130..9895750,2	K562	blood:
2	chr12:9889267..9893240-chr12:9909352..9912451,4	K562	blood:

Variant related genes	Relation type
CLECL1	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1008611	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743820	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10743821	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743822	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772104	0.81[ASN][1000 genomes]
rs10844418	0.83[ASN][1000 genomes]
rs10844424	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10844429	0.84[ASN][1000 genomes]
rs10844449	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10844457	0.84[ASN][1000 genomes]
rs10844476	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10844676	0.81[ASN][1000 genomes]
rs11052305	0.83[ASN][1000 genomes]
rs11052311	0.83[ASN][1000 genomes]
rs11052327	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11052342	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11052366	0.83[ASN][1000 genomes]
rs11052367	0.83[ASN][1000 genomes]
rs11052430	0.84[ASN][1000 genomes]
rs11052431	0.84[ASN][1000 genomes]
rs11052434	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11052718	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052771	0.81[ASN][1000 genomes]
rs11052785	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11519377	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11524523	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12309762	0.83[ASN][1000 genomes]
rs12320830	0.84[ASN][1000 genomes]
rs12368445	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12369995	0.83[ASN][1000 genomes]
rs12370579	0.83[ASN][1000 genomes]
rs12371503	0.83[ASN][1000 genomes]
rs12371981	0.83[ASN][1000 genomes]
rs12371982	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12578698	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578928	0.84[ASN][1000 genomes]
rs12809752	0.83[ASN][1000 genomes]
rs12810851	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12812783	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12814560	0.83[ASN][1000 genomes]
rs12815393	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12816660	0.83[ASN][1000 genomes]
rs12817365	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12817550	0.83[ASN][1000 genomes]
rs12817743	0.83[ASN][1000 genomes]
rs12818179	0.83[ASN][1000 genomes]
rs12819865	0.83[ASN][1000 genomes]
rs12820674	0.83[ASN][1000 genomes]
rs12823653	0.83[ASN][1000 genomes]
rs12823699	0.84[ASN][1000 genomes]
rs12825507	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12828602	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12828773	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12830448	0.83[ASN][1000 genomes]
rs12830867	0.83[ASN][1000 genomes]
rs12830878	0.83[ASN][1000 genomes]
rs12831453	0.84[ASN][1000 genomes]
rs1861089	0.83[ASN][1000 genomes]
rs1990533	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080207	0.83[ASN][1000 genomes]
rs2114872	0.84[ASN][1000 genomes]
rs2114873	0.84[ASN][1000 genomes]
rs2192433	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192434	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192435	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192439	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2401396	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136577	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3176792	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3176804	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3176807	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3176808	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34201389	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34279883	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34826829	0.83[ASN][1000 genomes]
rs34850016	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35078787	0.83[ASN][1000 genomes]
rs35210729	0.82[AMR][1000 genomes]
rs35237063	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs35494990	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35512621	0.83[ASN][1000 genomes]
rs4763264	0.83[ASN][1000 genomes]
rs4763280	0.83[ASN][1000 genomes]
rs4763814	0.83[ASN][1000 genomes]
rs4763819	0.83[ASN][1000 genomes]
rs4763835	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763865	0.81[ASN][1000 genomes]
rs4763867	0.81[ASN][1000 genomes]
rs61913428	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488109	0.83[ASN][1000 genomes]
rs6488122	0.84[ASN][1000 genomes]
rs66725265	0.83[ASN][1000 genomes]
rs67429242	0.83[ASN][1000 genomes]
rs71441764	0.83[ASN][1000 genomes]
rs7297324	0.81[ASN][1000 genomes]
rs7310897	0.84[ASN][1000 genomes]
rs7312624	0.81[ASN][1000 genomes]
rs7485402	0.83[ASN][1000 genomes]
rs7954062	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7961812	0.83[ASN][1000 genomes]
rs7961903	0.83[ASN][1000 genomes]
rs7969074	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7971721	0.81[ASN][1000 genomes]
rs7972035	0.83[ASN][1000 genomes]
rs7974554	0.83[ASN][1000 genomes]
rs7975557	0.83[ASN][1000 genomes]
rs7975865	0.83[ASN][1000 genomes]
rs7979758	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9630264	0.84[ASN][1000 genomes]
rs9630265	0.84[ASN][1000 genomes]
rs9668568	0.83[ASN][1000 genomes]
rs982511	0.86[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12582616	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9885000-9892000	Enhancers	Primary hematopoietic stem cells	blood
2	chr12:9885800-9890600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:9885800-9892400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr12:9886000-9890600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:9886000-9891800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:9886000-9892000	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:9886000-9894600	Enhancers	Primary B cells from cord blood	blood
8	chr12:9887600-9893800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:9889000-9890800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:9889000-9891400	Enhancers	Adipose Nuclei	Adipose
11	chr12:9889000-9891800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:9889000-9892000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:9889000-9892000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:9889000-9895200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:9889200-9890000	Enhancers	Fetal Lung	lung
16	chr12:9889200-9891400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:9889200-9891600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:9889200-9891800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:9889200-9892200	Weak transcription	Thymus	Thymus
20	chr12:9889400-9890000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr12:9889400-9890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:9889400-9890400	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:9889400-9890800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:9889400-9891000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:9889400-9891400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:9889400-9891600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:9889600-9889800	Enhancers	Fetal Thymus	thymus
28	chr12:9889600-9890000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr12:9889600-9890000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:9889600-9890200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:9889600-9890400	Enhancers	Dnd41	blood
32	chr12:9889600-9891600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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