Variant report

Variant	rs224575
Chromosome Location	chr12:51419621-51419622
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	TAF1	chr12:51419385-51419847	Hela-S3	cervix:	n/a	n/a
2	MYC	chr12:51419418-51420624	K562	blood:	n/a	chr12:51420284-51420293
3	MYC	chr12:51419575-51420564	MCF10A-Er-Src	breast:	n/a	chr12:51420284-51420293
4	TBP	chr12:51418482-51420562	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:51419609-51420595	A549	lung:	n/a	n/a
6	HEY1	chr12:51419372-51420639	K562	blood:	n/a	chr12:51419671-51419686
7	YY1	chr12:51419463-51420432	H1-hESC	embryonic stem cell:	n/a	chr12:51419673-51419687 chr12:51420119-51420128 chr12:51419818-51419827
8	POLR2A	chr12:51419332-51420527	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:51419459-51420690	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr12:51419237-51420765	HepG2	liver:	n/a	chr12:51420284-51420293
11	MAX	chr12:51419220-51420761	HepG2	liver:	n/a	chr12:51420284-51420293
12	TAF1	chr12:51419351-51420512	H1-hESC	embryonic stem cell:	n/a	n/a
13	NR2F2	chr12:51419233-51420321	K562	blood:	n/a	chr12:51420065-51420080
14	REST	chr12:51419428-51420082	HepG2	liver:	n/a	chr12:51419656-51419669
15	MYBL2	chr12:51418563-51420609	HepG2	liver:	n/a	n/a
16	CTCF	chr12:51419560-51419710	Hela-S3	cervix:	n/a	chr12:51419671-51419684
17	TBP	chr12:51419456-51420534	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:51419292-51420561	K562	blood:	n/a	n/a
19	POLR2A	chr12:51419274-51420729	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr12:51419519-51420602	GM18951	blood:	n/a	n/a
21	SIN3A	chr12:51419252-51420492	H1-hESC	embryonic stem cell:	n/a	chr12:51419656-51419669
22	E2F6	chr12:51419529-51420569	K562	blood:	n/a	chr12:51420120-51420130 chr12:51420190-51420199
23	E2F6	chr12:51419458-51420751	A549	lung:	n/a	chr12:51420120-51420130 chr12:51420190-51420199
24	MAX	chr12:51419506-51420697	HCT-116	colon:	n/a	chr12:51420284-51420293
25	TAF7	chr12:51419428-51420544	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:51419511-51420499	GM12878	blood:	n/a	n/a
27	TCF12	chr12:51419371-51420701	ECC-1	luminal epithelium:	n/a	chr12:51419498-51419506
28	NR2F2	chr12:51419397-51420654	MCF-7	breast:	n/a	chr12:51420065-51420080
29	ZMIZ1	chr12:51418620-51420513	K562	blood:	n/a	n/a
30	MAX	chr12:51419385-51420717	MCF-7	breast:	n/a	chr12:51420284-51420293
31	MAX	chr12:51419463-51420505	H1-hESC	embryonic stem cell:	n/a	chr12:51420284-51420293
32	MAX	chr12:51419511-51420602	H1-hESC	embryonic stem cell:	n/a	chr12:51420284-51420293
33	CHD2	chr12:51419177-51420477	HepG2	liver:	n/a	chr12:51420029-51420039
34	TEAD4	chr12:51419076-51419641	K562	blood:	n/a	n/a
35	POLR2A	chr12:51418173-51421529	HepG2	liver:	n/a	n/a
36	PML	chr12:51419546-51420581	GM12878	blood:	n/a	n/a
37	ESR1	chr12:51419524-51419928	ECC-1	luminal epithelium:	n/a	chr12:51419748-51419763
38	MAX	chr12:51419566-51420534	A549	lung:	n/a	chr12:51420284-51420293
39	POLR2A	chr12:51419442-51420538	Hela-S3	cervix:	n/a	n/a
40	TCF7L2	chr12:51419444-51420369	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr12:51419621-51419767	HUVEC	blood vessel:	n/a	n/a
42	EP300	chr12:51419576-51420337	ECC-1	luminal epithelium:	n/a	chr12:51420120-51420136 chr12:51420119-51420128 chr12:51419787-51419803
43	POLR2A	chr12:51419593-51420561	GM15510	blood:	n/a	n/a
44	TAF1	chr12:51419471-51420540	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:51418479-51420428	K562	blood:	n/a	n/a
46	RCOR1	chr12:51419523-51420598	K562	blood:	n/a	n/a
47	MAX	chr12:51419456-51420694	MCF-7	breast:	n/a	chr12:51420284-51420293
48	ESR1	chr12:51419402-51419958	ECC-1	luminal epithelium:	n/a	chr12:51419748-51419763
49	YY1	chr12:51419481-51420211	HepG2	liver:	n/a	chr12:51419673-51419687 chr12:51420119-51420128 chr12:51419818-51419827
50	POLR2A	chr12:51419425-51420608	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51393339..51395355-chr12:51418733..51421410,2	MCF-7	breast:
2	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
3	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
4	chr12:51419557..51420269-chr17:73150232..73151007,2	Hela-S3	cervix:
5	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
6	chr12:51157405..51159033-chr12:51418554..51420263,2	MCF-7	breast:
7	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
8	chr12:51418513..51423622-chr12:51474378..51479071,10	MCF-7	breast:
9	chr12:51419545..51420090-chr12:51477089..51478060,2	Hela-S3	cervix:
10	chr12:51419463..51422870-chr12:51476162..51478400,3	K562	blood:
11	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
12	chr12:51419291..51420223-chr12:51441428..51442247,3	MCF-7	breast:
13	chr12:51419574..51420267-chr12:51441420..51442175,2	Hela-S3	cervix:
14	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
15	chr12:50897880..50899909-chr12:51417990..51420226,2	MCF-7	breast:
16	chr12:51417478..51420284-chr12:51632474..51634014,2	MCF-7	breast:
17	chr12:51159439..51159963-chr12:51419339..51419854,2	MCF-7	breast:
18	chr12:51418648..51420255-chr12:51610985..51612931,2	K562	blood:
19	chr12:51418785..51420716-chr12:51421022..51423680,2	K562	blood:
20	chr12:51419621..51420148-chr19:13056676..13057213,2	Hela-S3	cervix:
21	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
22	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
23	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
24	chr12:51316948..51319607-chr12:51419309..51421732,3	K562	blood:
25	chr12:51316948..51319607-chr12:51419309..51421732,2	K562	blood:
26	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000066084	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000272028	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000179262	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000185432	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10783408	0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs10783409	0.85[CEU][hapmap]
rs10783410	0.96[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876123	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876128	0.85[CEU][hapmap]
rs10876130	0.81[CEU][hapmap]
rs10876131	0.84[CEU][hapmap]
rs10876136	0.81[CEU][hapmap]
rs12424509	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12809226	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12823317	0.85[ASN][1000 genomes]
rs149411	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs15756	0.85[CEU][hapmap]
rs1632791	0.84[CEU][hapmap]
rs2029145	0.87[CEU][hapmap]
rs2029146	0.85[CEU][hapmap]
rs224572	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs2359187	0.83[ASN][1000 genomes]
rs2544019	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554856	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319931	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319936	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319939	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs370462	0.85[CEU][hapmap]
rs427020	0.87[CEU][hapmap]
rs4438107	0.81[CEU][hapmap]
rs6580782	0.84[CEU][hapmap]
rs6580785	0.81[CEU][hapmap]
rs6580788	0.81[CEU][hapmap]
rs7961626	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs829017	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs224575	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs224575	SRSF2IP	cis	parietal	SCAN
rs224575	CSRNP2	cis	cerebellum	SCAN
rs224575	COL2A1	cis	cerebellum	SCAN
rs224575	DDN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51417200-51419800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:51417400-51420600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr12:51417400-51420800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:51417600-51419800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr12:51417600-51420000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:51417800-51419800	Active TSS	Right Atrium	heart
7	chr12:51417800-51419800	Flanking Active TSS	HUVEC	blood vessel
8	chr12:51417800-51420200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:51417800-51420600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:51417800-51420600	Active TSS	Aorta	Aorta
11	chr12:51417800-51420800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:51417800-51420800	Active TSS	Brain Angular Gyrus	brain
13	chr12:51418000-51419800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr12:51418000-51419800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr12:51418000-51420000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:51418000-51420400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:51418000-51420400	Active TSS	NHLF	lung
18	chr12:51418000-51420600	Active TSS	Brain Anterior Caudate	brain
19	chr12:51418000-51420600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:51418000-51420600	Active TSS	Right Ventricle	heart
21	chr12:51418000-51420800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:51418200-51420200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:51418200-51420400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:51418200-51420400	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr12:51418200-51420400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:51418200-51420400	Active TSS	Brain Cingulate Gyrus	brain
27	chr12:51418200-51420400	Active TSS	Brain Substantia Nigra	brain
28	chr12:51418200-51420400	Active TSS	K562	blood
29	chr12:51418200-51420600	Active TSS	Esophagus	oesophagus
30	chr12:51418200-51420600	Active TSS	Ovary	ovary
31	chr12:51418200-51420600	Active TSS	Psoas Muscle	Psoas
32	chr12:51418200-51420600	Active TSS	Stomach Mucosa	stomach
33	chr12:51418200-51421200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:51418400-51419800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr12:51418400-51420000	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:51418400-51420400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:51418400-51420400	Active TSS	Fetal Intestine Large	intestine
38	chr12:51418400-51420600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:51418400-51420600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:51418400-51420600	Active TSS	Brain Hippocampus Middle	brain
41	chr12:51418400-51420600	Active TSS	Left Ventricle	heart
42	chr12:51418600-51420400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:51418600-51420400	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:51418600-51420600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:51418600-51420600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr12:51418800-51419800	Active TSS	Brain Germinal Matrix	brain
47	chr12:51418800-51420000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr12:51418800-51420400	Active TSS	H1 Cell Line	embryonic stem cell
49	chr12:51418800-51420400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr12:51418800-51420400	Active TSS	Fetal Brain Male	brain

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