Variant report

Variant	rs10492166
Chromosome Location	chr12:9885999-9886000
allele	A/G
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	MTA3	chr12:9885081-9886221	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr12:9885378-9886161	GM12878	blood:	n/a	n/a
3	SPI1	chr12:9885515-9886219	GM12891	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
4	STAT3	chr12:9885585-9886002	GM12878	blood:	n/a	n/a
5	SPI1	chr12:9885614-9886110	GM12878	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
6	SPI1	chr12:9885717-9886245	HL-60	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
7	REST	chr12:9885802-9886089	Hela-S3	cervix:	n/a	n/a
8	NFATC1	chr12:9885361-9886140	GM12878	blood:	n/a	n/a
9	BCLAF1	chr12:9885400-9886135	GM12878	blood:	n/a	n/a
10	BHLHE40	chr12:9885577-9886144	GM12878	blood:	n/a	n/a
11	TBP	chr12:9885403-9886055	GM12878	blood:	n/a	n/a
12	EP300	chr12:9885511-9886136	GM12878	blood:	n/a	chr12:9885964-9885973
13	NFIC	chr12:9884090-9886395	GM12878	blood:	n/a	n/a
14	SPI1	chr12:9885855-9886061	K562	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
15	CUX1	chr12:9885653-9886194	GM12878	blood:	n/a	n/a
16	STAT5A	chr12:9885320-9886062	GM12878	blood:	n/a	n/a
17	SPI1	chr12:9885816-9886072	K562	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
18	RUNX3	chr12:9885429-9886155	GM12878	blood:	n/a	n/a
19	PML	chr12:9885310-9886145	GM12878	blood:	n/a	n/a
20	ATF2	chr12:9885386-9886178	GM12878	blood:	n/a	n/a
21	NFIC	chr12:9885320-9886334	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:9885280-9886029	GM12892	blood:	n/a	n/a
23	CHD1	chr12:9883753-9886167	GM12878	blood:	n/a	n/a
24	EP300	chr12:9885624-9886015	GM12878	blood:	n/a	chr12:9885964-9885973
25	BATF	chr12:9885494-9885999	GM12878	blood:	n/a	n/a
26	NFATC1	chr12:9885389-9886055	GM12878	blood:	n/a	n/a
27	CREB1	chr12:9885283-9886119	GM12878	blood:	n/a	n/a
28	IKZF1	chr12:9885648-9886206	GM12878	blood:	n/a	chr12:9886043-9886051
29	STAT5A	chr12:9885516-9886036	GM12878	blood:	n/a	n/a
30	SPI1	chr12:9885663-9886105	GM12878	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
31	RCOR1	chr12:9885561-9886059	GM12878	blood:	n/a	n/a
32	EBF1	chr12:9885485-9886043	GM12878	blood:	n/a	n/a
33	EP300	chr12:9885167-9886068	GM12878	blood:	n/a	chr12:9885964-9885973
34	STAT3	chr12:9885866-9886060	MCF10A-Er-Src	breast:	n/a	n/a
35	ATF2	chr12:9885601-9886061	GM12878	blood:	n/a	n/a
36	FOXM1	chr12:9885396-9886119	GM12878	blood:	n/a	n/a
37	SPI1	chr12:9885583-9886180	HL-60	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
38	RUNX3	chr12:9885382-9886107	GM12878	blood:	n/a	n/a
39	SPI1	chr12:9885386-9886414	GM12878	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
40	SPI1	chr12:9885588-9886163	GM12891	blood:	n/a	chr12:9885965-9885972 chr12:9885962-9885975 chr12:9885964-9885973 chr12:9885963-9885976
41	RELA	chr12:9885136-9886098	GM19099	blood:	n/a	n/a
42	MEF2A	chr12:9885423-9886091	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:9885998-9886048	GM12891	blood:	n/a
2	chr12:9885998-9886048	HepG2	liver:	n/a
3	chr12:9885998-9886048	PANC-1	pancreas:	n/a
4	chr12:9885998-9886048	GM19239	blood:	n/a
5	chr12:9885998-9886048	HEEpiC	esophagus:	n/a
6	chr12:9885998-9886048	Hela-S3	cervix:	n/a
7	chr12:9885998-9886048	HRPEpiC	eye:	n/a
8	chr12:9885998-9886048	AG09319	gingival:	n/a
9	chr12:9885998-9886048	GM12892	blood:	n/a
10	chr12:9885998-9886048	T-47D	breast:	n/a
11	chr12:9885998-9886048	AG09309	skin:	n/a
12	chr12:9885998-9886048	HRE	kidney:	n/a
13	chr12:9885998-9886048	ECC-1	luminal epithelium:	n/a
14	chr12:9885998-9886048	NT2-D1	testis:	n/a
15	chr12:9885998-9886048	HRCEpiC	kidney:	n/a
16	chr12:9885998-9886048	AoSMC	blood vessel:	n/a
17	chr12:9885998-9886048	AG04449	skin:	fetal
18	chr12:9885998-9886048	SK-N-SH_RA	brain:	n/a
19	chr12:9885998-9886048	H1-hESC	embryonic stem cell:	embryo
20	chr12:9885998-9886048	NHBE	bronchial:	n/a
21	chr12:9885998-9886048	PFSK-1	brain:	n/a
22	chr12:9885998-9886048	HIPEpiC	eye:	n/a
23	chr12:9885998-9886048	MCF10A-Er-Src	breast:	n/a
24	chr12:9885998-9886048	ProgFib	skin:	n/a
25	chr12:9885998-9886048	Caco-2	colon:	n/a
26	chr12:9885998-9886048	HL-60	blood:	n/a
27	chr12:9885998-9886048	HCT-116	colon:	n/a
28	chr12:9885998-9886048	SK-N-MC	brain:	n/a
29	chr12:9885998-9886048	MCF-7	breast:	n/a
30	chr12:9885998-9886048	BJ	skin:	n/a
31	chr12:9885998-9886048	HCF	heart:	n/a
32	chr12:9885998-9886048	HUVEC	blood vessel:	n/a
33	chr12:9885998-9886048	GM12878	blood:	n/a
34	chr12:9885998-9886048	Jurkat	blood:	n/a
35	chr12:9885998-9886048	RPTEC	kidney:	n/a
36	chr12:9885998-9886048	A549	lung:	n/a
37	chr12:9885998-9886048	Hepatocyte	liver:	n/a
38	chr12:9885998-9886048	HCPEpiC	choroid plexus:	n/a
39	chr12:9885998-9886048	AG04450	lung:	fetal
40	chr12:9885998-9886048	SAEC	small airway:	n/a
41	chr12:9885998-9886048	HPAEpiC	pulmonary alveolar:	n/a
42	chr12:9885998-9886048	BE2_C	brain:	n/a
43	chr12:9885998-9886048	K562	blood:	n/a
44	chr12:9885998-9886048	CMK	blood:	n/a
45	chr12:9885998-9886048	GM06990	blood:	n/a
46	chr12:9885998-9886048	HMEC	breast:	n/a
47	chr12:9885998-9886048	U87	brain:	n/a
48	chr12:9885998-9886048	IMR90	lung:	fetal
49	chr12:9885998-9886048	LNCaP	prostate:	n/a
50	chr12:9885998-9886048	NB4	blood:	n/a

Variant related genes	Relation type
CLECL1	TF binding region
CLECL1	CpG island

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1008610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1044771	0.85[JPT][hapmap]
rs10466829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10492165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743819	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743823	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10772046	0.88[ASN][1000 genomes]
rs10772062	0.90[ASN][1000 genomes]
rs10772070	0.95[ASN][1000 genomes]
rs10772071	0.95[ASN][1000 genomes]
rs10772072	0.95[ASN][1000 genomes]
rs10772073	0.95[ASN][1000 genomes]
rs10772074	0.95[ASN][1000 genomes]
rs10772079	0.95[ASN][1000 genomes]
rs10772085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10772090	0.94[ASN][1000 genomes]
rs10772091	0.96[ASN][1000 genomes]
rs10772092	0.96[ASN][1000 genomes]
rs10772094	0.96[ASN][1000 genomes]
rs10772102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772108	0.87[ASN][1000 genomes]
rs10844456	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10844468	0.88[ASN][1000 genomes]
rs10844503	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10844537	0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10844562	0.92[ASN][1000 genomes]
rs10844569	0.95[ASN][1000 genomes]
rs10844597	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10844609	0.95[ASN][1000 genomes]
rs10844610	0.94[ASN][1000 genomes]
rs10844615	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10844617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10844622	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844626	0.96[ASN][1000 genomes]
rs10844627	0.96[ASN][1000 genomes]
rs10844630	0.96[ASN][1000 genomes]
rs10844632	0.96[ASN][1000 genomes]
rs10844633	0.96[ASN][1000 genomes]
rs10844635	0.96[ASN][1000 genomes]
rs10844636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844637	0.95[ASN][1000 genomes]
rs10844638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844639	0.91[ASN][1000 genomes]
rs10844640	0.87[ASN][1000 genomes]
rs10844657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10844682	0.87[ASN][1000 genomes]
rs10844706	0.91[JPT][hapmap]
rs11052372	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052423	0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11052426	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11052552	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11052604	0.90[ASN][1000 genomes]
rs11052710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11052713	0.94[ASN][1000 genomes]
rs11052717	0.95[ASN][1000 genomes]
rs11052750	0.96[ASN][1000 genomes]
rs11052751	0.96[ASN][1000 genomes]
rs11052752	0.96[ASN][1000 genomes]
rs11052756	0.90[ASN][1000 genomes]
rs11052877	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12227655	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12228641	0.91[ASN][1000 genomes]
rs12304510	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317499	0.97[ASN][1000 genomes]
rs17806710	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1985788	0.85[ASN][1000 genomes]
rs2058560	0.95[ASN][1000 genomes]
rs2080206	0.81[ASN][1000 genomes]
rs2080211	0.85[JPT][hapmap]
rs2098298	0.94[JPT][hapmap]
rs2114870	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2192437	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2268146	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2401390	0.95[ASN][1000 genomes]
rs2401391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401394	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401395	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764021	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3764022	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4763839	0.87[ASN][1000 genomes]
rs4763840	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4763879	0.82[JPT][hapmap]
rs7296241	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7306304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307111	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310460	0.85[JPT][hapmap]
rs741199	0.95[ASN][1000 genomes]
rs741200	0.86[ASN][1000 genomes]
rs7956831	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968401	0.87[ASN][1000 genomes]
rs7970116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973535	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974396	0.90[JPT][hapmap]
rs7976584	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977720	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917911	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10492166	CLECL1	cis	lung	GTEx
rs10492166	CLECL1	cis	Nerve Tibial	GTEx
rs10492166	CLECL1	cis	Adipose Subcutaneous	GTEx
rs10492166	CLECL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9878600-9886000	Active TSS	GM12878-XiMat	blood
2	chr12:9883200-9886000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:9883400-9886000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr12:9884000-9886000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:9884800-9886000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
6	chr12:9884800-9886000	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr12:9884800-9886800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:9884800-9887200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:9885000-9892000	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:9885400-9886000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:9885600-9886000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:9885600-9886200	Enhancers	Primary T cells from cord blood	blood
13	chr12:9885600-9886200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:9885600-9886200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:9885600-9886200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:9885800-9886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:9885800-9886200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:9885800-9886200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:9885800-9886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:9885800-9886800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:9885800-9889200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:9885800-9889400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:9885800-9889600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:9885800-9890600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:9885800-9892400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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