Variant report

Variant	rs2466145
Chromosome Location	chr12:122150383-122150384
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	POLR2A	chr12:122150017-122150974	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:122150243-122150695	SK-N-MC	brain:	n/a	n/a
3	MAX	chr12:122150343-122151301	SK-N-SH	brain:	n/a	chr12:122151243-122151253 chr12:122151055-122151064 chr12:122150725-122150734 chr12:122150663-122150672
4	PBX3	chr12:122149948-122150868	A549	lung:	n/a	n/a
5	IRF1	chr12:122150357-122150878	K562	blood:	n/a	chr12:122150572-122150586 chr12:122150577-122150591
6	ZBTB7A	chr12:122150362-122150547	HepG2	liver:	n/a	n/a
7	MAX	chr12:122150027-122151289	NB4	blood:	n/a	chr12:122151243-122151253 chr12:122151055-122151064 chr12:122150725-122150734 chr12:122150663-122150672
8	MAX	chr12:122150143-122151248	MCF-7	breast:	n/a	chr12:122151055-122151064 chr12:122150725-122150734 chr12:122150663-122150672
9	POLR2A	chr12:122149887-122150990	GM12892	blood:	n/a	n/a
10	TAF1	chr12:122150367-122150988	HepG2	liver:	n/a	n/a
11	YY1	chr12:122150236-122150936	GM12892	blood:	n/a	chr12:122150732-122150743 chr12:122150713-122150727 chr12:122150246-122150260 chr12:122150772-122150786
12	POLR2A	chr12:122150336-122150920	HepG2	liver:	n/a	n/a
13	GTF2F1	chr12:122150197-122150550	Hela-S3	cervix:	n/a	n/a
14	HCFC1	chr12:122150065-122151116	K562	blood:	n/a	n/a
15	TAF1	chr12:122149946-122150675	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr12:122150260-122150937	GM12878	blood:	n/a	chr12:122150732-122150743 chr12:122150713-122150727 chr12:122150772-122150786
17	TBP	chr12:122150322-122150687	HepG2	liver:	n/a	n/a
18	ZBTB7A	chr12:122150143-122151510	ECC-1	luminal epithelium:	n/a	chr12:122151397-122151411
19	RUNX3	chr12:122150351-122150936	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:122150210-122150623	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:122150288-122150659	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYBL2	chr12:122150183-122150668	HepG2	liver:	n/a	n/a
23	POU2F2	chr12:122150281-122150663	GM12891	blood:	n/a	n/a
24	JUND	chr12:122150008-122150509	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPD	chr12:122150274-122150692	HepG2	liver:	n/a	n/a
26	HDAC2	chr12:122150072-122150555	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:122150151-122151180	A549	lung:	n/a	n/a
28	POLR2A	chr12:122150264-122150878	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:122150348-122150596	GM12891	blood:	n/a	n/a
30	POLR2A	chr12:122150213-122151090	MCF-7	breast:	n/a	n/a
31	SIN3AK20	chr12:122149953-122150596	A549	lung:	n/a	n/a
32	POLR2A	chr12:122150079-122150901	K562	blood:	n/a	n/a
33	MAX	chr12:122150223-122151206	GM12878	blood:	n/a	chr12:122151055-122151064 chr12:122150725-122150734 chr12:122150663-122150672
34	POLR2A	chr12:122150228-122151265	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr12:122150197-122150888	GM12878	blood:	n/a	n/a
36	STAT5A	chr12:122150262-122150593	GM12878	blood:	n/a	chr12:122150464-122150473 chr12:122150575-122150587 chr12:122150465-122150474
37	SIN3AK20	chr12:122149852-122151405	MCF-7	breast:	n/a	n/a
38	POLR2A	chr12:122150200-122150876	K562	blood:	n/a	n/a
39	POLR2A	chr12:122150308-122150959	GM12891	blood:	n/a	n/a
40	CEBPB	chr12:122150357-122150946	Hela-S3	cervix:	n/a	n/a
41	ZC3H11A	chr12:122150052-122150475	K562	blood:	n/a	n/a
42	YY1	chr12:122150301-122150749	SK-N-SH_RA	brain:	n/a	chr12:122150732-122150743 chr12:122150713-122150727
43	BHLHE40	chr12:122150284-122150831	HepG2	liver:	n/a	chr12:122150767-122150783
44	POU2F2	chr12:122150201-122150737	GM12878	blood:	n/a	n/a
45	MAX	chr12:122150343-122151418	H1-hESC	embryonic stem cell:	n/a	chr12:122151243-122151253 chr12:122151055-122151064 chr12:122150725-122150734 chr12:122150663-122150672
46	MAZ	chr12:122149925-122152630	IMR90	lung:	n/a	chr12:122151934-122151943 chr12:122151932-122151943 chr12:122151933-122151942 chr12:122151243-122151253 chr12:122151931-122151944 chr12:122151055-122151064 chr12:122151932-122151943 chr12:122150725-122150734 chr12:122151932-122151942 chr12:122150663-122150672 chr12:122151931-122151944
47	POLR2A	chr12:122150112-122151103	SK-N-MC	brain:	n/a	n/a
48	ELF1	chr12:122149905-122150752	K562	blood:	n/a	n/a
49	PML	chr12:122149902-122150678	K562	blood:	n/a	n/a
50	POLR2A	chr12:122150119-122150940	GM18951	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:122150344-122150394	HPAEpiC	pulmonary alveolar:	n/a
2	chr12:122150344-122150394	NH-A	brain:	n/a
3	chr12:122150344-122150394	GM12892	blood:	n/a
4	chr12:122150344-122150394	IMR90	lung:	fetal
5	chr12:122150344-122150394	GM12891	blood:	n/a
6	chr12:122150344-122150394	H1-hESC	embryonic stem cell:	embryo
7	chr12:122150344-122150394	HNPCEpiC	eye:	n/a
8	chr12:122150344-122150394	A549	lung:	n/a
9	chr12:122150344-122150394	AG09309	skin:	n/a
10	chr12:122150344-122150394	SAEC	small airway:	n/a
11	chr12:122150344-122150394	HRPEpiC	eye:	n/a
12	chr12:122150344-122150394	BJ	skin:	n/a
13	chr12:122150344-122150394	NB4	blood:	n/a
14	chr12:122150344-122150394	AG10803	skin:	n/a
15	chr12:122150344-122150394	Hela-S3	cervix:	n/a
16	chr12:122150344-122150394	SK-N-MC	brain:	n/a
17	chr12:122150344-122150394	HL-60	blood:	n/a
18	chr12:122150344-122150394	GM12878	blood:	n/a
19	chr12:122150344-122150394	LNCaP	prostate:	n/a
20	chr12:122150344-122150394	AoSMC	blood vessel:	n/a
21	chr12:122150344-122150394	Hepatocyte	liver:	n/a
22	chr12:122150344-122150394	HEEpiC	esophagus:	n/a
23	chr12:122150344-122150394	PANC-1	pancreas:	n/a
24	chr12:122150344-122150394	HEK293	kidney:	embryo
25	chr12:122150344-122150394	ECC-1	luminal epithelium:	n/a
26	chr12:122150344-122150394	HCT-116	colon:	n/a
27	chr12:122150344-122150394	MCF-7	breast:	n/a
28	chr12:122150344-122150394	Caco-2	colon:	n/a
29	chr12:122150344-122150394	NHBE	bronchial:	n/a
30	chr12:122150344-122150394	NHDF-neo	bronchial:	n/a
31	chr12:122150344-122150394	Jurkat	blood:	n/a
32	chr12:122150344-122150394	HRCEpiC	kidney:	n/a
33	chr12:122150344-122150394	NT2-D1	testis:	n/a
34	chr12:122150344-122150394	T-47D	breast:	n/a
35	chr12:122150344-122150394	U87	brain:	n/a
36	chr12:122150344-122150394	HRE	kidney:	n/a
37	chr12:122150344-122150394	BE2_C	brain:	n/a
38	chr12:122150344-122150394	HMEC	breast:	n/a
39	chr12:122150344-122150394	AG09319	gingival:	n/a
40	chr12:122150344-122150394	HAEpiC	amniotic membrane:	n/a
41	chr12:122150344-122150394	PFSK-1	brain:	n/a
42	chr12:122150344-122150394	CMK	blood:	n/a
43	chr12:122150344-122150394	HCF	heart:	n/a
44	chr12:122150344-122150394	AG04449	skin:	fetal
45	chr12:122150344-122150394	GM06990	blood:	n/a
46	chr12:122150344-122150394	ProgFib	skin:	n/a
47	chr12:122150344-122150394	K562	blood:	n/a
48	chr12:122150344-122150394	PrEC	prostate:	n/a
49	chr12:122150344-122150394	AG04450	lung:	fetal
50	chr12:122150344-122150394	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122148895..122150482-chr12:122213569..122215143,2	K562	blood:
2	chr12:122148985..122154094-chr12:122210649..122217008,11	MCF-7	breast:
3	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
4	chr12:122148639..122153380-chr12:122238008..122242328,5	MCF-7	breast:
5	chr12:122149069..122151072-chr12:122242291..122244324,2	MCF-7	breast:
6	chr11:85955821..85956367-chr12:122150370..122150929,2	NB4	blood:
7	chr12:122147215..122155218-chr12:122185094..122190846,22	MCF-7	breast:
8	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
9	chr12:121974472..121977117-chr12:122150068..122152069,2	MCF-7	breast:
10	chr12:122150220..122151057-chr6:26188979..26189750,2	NB4	blood:
11	chr11:62420365..62421322-chr12:122150183..122150817,2	NB4	blood:
12	chr12:122150096..122150704-chr7:98922914..98923914,2	NB4	blood:

Variant related genes	Relation type
TMEM120B	TF binding region
TMEM120B	CpG island
ENSG00000185085	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000074266	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000188987	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10770182	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs10840612	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043180	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12320939	0.80[MEX][hapmap]
rs2137434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458402	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2669166	0.84[MEX][hapmap]
rs2720022	0.80[MEX][hapmap]
rs2720041	0.80[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs2942368	0.80[MEX][hapmap]
rs2942370	0.80[CEU][hapmap]
rs2942379	0.80[MEX][hapmap]
rs2954111	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2954112	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967415	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs925531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2466145	LRRC43	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122149400-122150400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr12:122149400-122150400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr12:122149400-122150400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:122149400-122150400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr12:122149400-122150400	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr12:122149400-122151800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:122149600-122150400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr12:122149600-122150400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:122149600-122150400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:122149600-122150400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:122149600-122150400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:122149600-122150400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:122149600-122150400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr12:122149600-122150400	Flanking Active TSS	Osteobl	bone
15	chr12:122149600-122150800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:122149600-122150800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:122149600-122151000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:122149600-122151000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr12:122149600-122151200	Active TSS	Left Ventricle	heart
20	chr12:122149600-122151200	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:122149600-122151200	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:122149600-122151400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:122149600-122151400	Active TSS	Pancreas	Pancrea
24	chr12:122149600-122151400	Active TSS	Right Atrium	heart
25	chr12:122149600-122151600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr12:122149600-122151800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:122149600-122152200	Active TSS	HSMM	muscle
28	chr12:122149800-122150400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:122149800-122150400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:122149800-122150400	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:122149800-122150400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:122149800-122150400	Flanking Active TSS	Dnd41	blood
33	chr12:122149800-122150400	Flanking Active TSS	Hela-S3	cervix
34	chr12:122149800-122150400	Flanking Active TSS	HUVEC	blood vessel
35	chr12:122149800-122150400	Flanking Active TSS	NH-A	brain
36	chr12:122149800-122150400	Flanking Active TSS	NHEK	skin
37	chr12:122149800-122150600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr12:122149800-122150800	Active TSS	Brain Germinal Matrix	brain
39	chr12:122149800-122150800	Active TSS	Colonic Mucosa	Colon
40	chr12:122149800-122150800	Active TSS	Lung	lung
41	chr12:122149800-122151000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:122149800-122151000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:122149800-122151000	Active TSS	Fetal Heart	heart
44	chr12:122149800-122151000	Active TSS	Placenta	Placenta
45	chr12:122149800-122151200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:122149800-122151200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:122149800-122151200	Active TSS	Esophagus	oesophagus
48	chr12:122149800-122151200	Active TSS	Fetal Brain Male	brain
49	chr12:122149800-122151200	Active TSS	Fetal Brain Female	brain
50	chr12:122149800-122151200	Active TSS	Right Ventricle	heart

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