Variant report

Variant	rs12423207
Chromosome Location	chr12:51422571-51422572
allele	C/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	CEBPB	chr12:51421872-51423020	Hela-S3	cervix:	n/a	n/a
2	TBP	chr12:51421861-51423004	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr12:51421842-51423374	MCF-7	breast:	n/a	chr12:51422084-51422095 chr12:51422150-51422158
4	CHD2	chr12:51421895-51423100	Hela-S3	cervix:	n/a	n/a
5	GATA3	chr12:51421822-51422971	T-47D	breast:	n/a	chr12:51422084-51422095 chr12:51422150-51422158
6	CTCF	chr12:51421695-51423014	A549	lung:	n/a	n/a
7	NR2F2	chr12:51421859-51422921	MCF-7	breast:	n/a	n/a
8	GATA3	chr12:51421873-51422910	T-47D	breast:	n/a	chr12:51422084-51422095 chr12:51422150-51422158
9	CEBPB	chr12:51422321-51422964	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:51421848-51422923	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr12:51421850-51423004	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr12:51421947-51423008	Hela-S3	cervix:	n/a	chr12:51422137-51422145
13	TCF12	chr12:51421858-51422748	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr12:51421631-51422877	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr12:51422523-51422941	T-47D	breast:	n/a	chr12:51422664-51422678
16	TFAP2C	chr12:51421930-51423373	Hela-S3	cervix:	n/a	chr12:51423155-51423170 chr12:51422768-51422783
17	TFAP2A	chr12:51421933-51423255	Hela-S3	cervix:	n/a	chr12:51422770-51422784 chr12:51422772-51422782 chr12:51422770-51422784 chr12:51422768-51422783
18	RAD21	chr12:51421819-51422915	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr12:51421862-51422928	Hela-S3	cervix:	n/a	n/a
20	RFX5	chr12:51421884-51423076	Hela-S3	cervix:	n/a	n/a
21	MAFK	chr12:51421922-51423011	Hela-S3	cervix:	n/a	chr12:51422544-51422555
22	MAZ	chr12:51421890-51422959	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr12:51422004-51422692	MCF10A-Er-Src	breast:	n/a	chr12:51422137-51422145
24	TCF7L2	chr12:51421904-51422980	Hela-S3	cervix:	n/a	n/a
25	MYC	chr12:51422492-51422924	MCF10A-Er-Src	breast:	n/a	n/a
26	GTF3C2	chr12:51421820-51422611	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr12:51422479-51422985	MCF-7	breast:	n/a	n/a
28	BRCA1	chr12:51421893-51422969	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr12:51422503-51423011	MCF-7	breast:	n/a	n/a
30	RCOR1	chr12:51421807-51423091	Hela-S3	cervix:	n/a	n/a
31	GATA3	chr12:51421751-51423217	MCF-7	breast:	n/a	chr12:51422084-51422095 chr12:51422150-51422158
32	RAD21	chr12:51421739-51422663	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr12:51421867-51422888	Hela-S3	cervix:	n/a	n/a
34	MXI1	chr12:51421904-51422879	Hela-S3	cervix:	n/a	n/a
35	MAX	chr12:51421887-51422902	Hela-S3	cervix:	n/a	n/a
36	NR2F2	chr12:51421805-51423445	MCF-7	breast:	n/a	n/a
37	ZKSCAN1	chr12:51421888-51422909	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51156398..51158646-chr12:51422122..51423732,2	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	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
5	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
6	chr12:51418513..51423622-chr12:51474378..51479071,10	MCF-7	breast:
7	chr12:51419815..51423306-chr17:56706440..56710556,3	MCF-7	breast:
8	chr12:51419463..51422870-chr12:51476162..51478400,3	K562	blood:
9	chr12:51422213..51424368-chr12:51428694..51432123,3	MCF-7	breast:
10	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
11	chr12:51418785..51420716-chr12:51421022..51423680,2	K562	blood:
12	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
13	chr12:51420182..51422992-chr12:51631104..51633893,3	MCF-7	breast:
14	chr12:51421116..51422954-chr12:51442627..51444321,2	K562	blood:
15	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:
16	chr12:51422336..51422886-chr14:75745086..75745607,2	Hela-S3	cervix:
17	chr12:51422433..51425067-chr12:51426862..51428458,2	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000183283	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000199903	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1026994	1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	1.00[ASN][1000 genomes]
rs10783412	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10876126	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.81[AMR][1000 genomes]
rs11169679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169718	1.00[JPT][hapmap]
rs11169724	1.00[JPT][hapmap]
rs12369066	1.00[JPT][hapmap]
rs150909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125367	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125370	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125416	1.00[JPT][hapmap]
rs17125418	1.00[JPT][hapmap]
rs17125428	1.00[JPT][hapmap]
rs17229232	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029147	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046498	0.82[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.94[EUR][1000 genomes]
rs224586	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.91[AMR][1000 genomes]
rs2554859	0.95[AMR][1000 genomes]
rs2630358	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630366	0.86[AMR][1000 genomes]
rs2630367	0.86[AMR][1000 genomes]
rs319930	0.86[AMR][1000 genomes]
rs319938	0.86[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap]
rs364627	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768959	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4768973	1.00[JPT][hapmap]
rs55874852	0.86[AMR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.90[EUR][1000 genomes]
rs6580783	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs686528	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7138860	0.82[AMR][1000 genomes]
rs7299484	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[JPT][hapmap]
rs7968372	0.80[EUR][1000 genomes]
rs7969536	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7975628	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs829021	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.92[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12423207	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51420200-51423000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:51420600-51422600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr12:51420600-51422600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr12:51420600-51422600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:51420600-51422800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:51420600-51422800	Enhancers	Fetal Thymus	thymus
7	chr12:51420600-51423800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:51420600-51423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:51421200-51422600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:51421200-51423200	Flanking Active TSS	Hela-S3	cervix
11	chr12:51421400-51422600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:51421400-51422800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:51421400-51423000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:51421600-51422800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:51421600-51422800	Active TSS	Fetal Intestine Large	intestine
16	chr12:51421600-51423000	Active TSS	Fetal Intestine Small	intestine
17	chr12:51421800-51422600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr12:51421800-51422800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:51421800-51422800	Enhancers	Stomach Mucosa	stomach
20	chr12:51421800-51422800	Flanking Active TSS	NHEK	skin
21	chr12:51422000-51422600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:51422000-51422600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:51422000-51422800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:51422000-51422800	Flanking Active TSS	A549	lung
25	chr12:51422000-51423200	Active TSS	Duodenum Mucosa	Duodenum
26	chr12:51422200-51422600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:51422200-51422600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:51422200-51422600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:51422200-51422600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:51422200-51422600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:51422200-51422600	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:51422200-51422600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:51422200-51422600	Enhancers	Liver	Liver
34	chr12:51422200-51422600	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr12:51422200-51422600	Flanking Active TSS	Osteobl	bone
36	chr12:51422200-51422800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr12:51422200-51422800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:51422200-51422800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr12:51422200-51422800	Flanking Active TSS	HMEC	breast
40	chr12:51422200-51423000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:51422400-51422600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:51422400-51422600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr12:51422400-51422600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:51422400-51422600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:51422400-51422600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:51422400-51422600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:51422400-51422600	Enhancers	Fetal Kidney	kidney
48	chr12:51422400-51422800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr12:51422400-51422800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr12:51422400-51422800	Flanking Active TSS	Placenta	Placenta

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