Variant report

Variant	rs224569
Chromosome Location	chr12:51386839-51386840
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	NFIC	chr12:51386541-51386969	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr12:51386700-51386850	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51385408..51389476-chr12:51420028..51421870,3	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

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[YRI][hapmap];1.00[ASN][1000 genomes]
rs10876126	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.95[AMR][1000 genomes]
rs11169679	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169718	1.00[JPT][hapmap]
rs11169724	1.00[JPT][hapmap]
rs12369066	1.00[JPT][hapmap]
rs12423207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814178	0.81[AFR][1000 genomes]
rs150909	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs2029147	1.00[ASN][1000 genomes]
rs2046498	0.82[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs224586	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.86[AMR][1000 genomes]
rs2554859	0.90[AMR][1000 genomes]
rs2554861	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630353	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2630362	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630366	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630367	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319930	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319938	0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs319940	0.82[EUR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319944	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs364627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768959	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768967	0.81[YRI][hapmap]
rs4768973	1.00[JPT][hapmap]
rs55874852	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.85[EUR][1000 genomes]
rs6580779	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6580783	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs686528	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.82[CEU][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7138860	0.86[EUR][1000 genomes]
rs7299484	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[JPT][hapmap]
rs7969536	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.85[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.86[AMR][1000 genomes]
rs7975628	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	1.00[YRI][hapmap]
rs829016	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs829021	0.82[CEU][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs853236	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9739943	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs224569	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL
rs224569	SLC11A2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51378000-51401800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:51378400-51391200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:51378600-51393200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:51378600-51399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:51378800-51396000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51379400-51396000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:51379400-51396200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:51379600-51389200	Weak transcription	Fetal Heart	heart
9	chr12:51379600-51395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:51379800-51391000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:51379800-51394600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:51379800-51396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:51380000-51387200	Strong transcription	Hela-S3	cervix
14	chr12:51380000-51396200	Strong transcription	Dnd41	blood
15	chr12:51380200-51387200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:51380200-51391400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:51380200-51396400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:51380200-51396600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:51380400-51387200	Strong transcription	Primary T cells from cord blood	blood
22	chr12:51380400-51391400	Strong transcription	Brain Germinal Matrix	brain
23	chr12:51380400-51396200	Strong transcription	Fetal Brain Female	brain
24	chr12:51380400-51396200	Strong transcription	Placenta	Placenta
25	chr12:51380600-51390800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:51380800-51391600	Strong transcription	Left Ventricle	heart
28	chr12:51381200-51391200	Strong transcription	Brain Hippocampus Middle	brain
29	chr12:51381200-51391400	Strong transcription	Colon Smooth Muscle	Colon
30	chr12:51381200-51392200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:51381200-51395800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
33	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
34	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:51381400-51391000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr12:51381400-51394200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:51381400-51396400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr12:51381600-51391000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr12:51381800-51391200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:51381800-51391400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr12:51381800-51391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:51381800-51402400	Strong transcription	Liver	Liver
47	chr12:51382000-51387000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:51382000-51387200	Strong transcription	Esophagus	oesophagus
49	chr12:51382000-51390800	Strong transcription	Right Ventricle	heart
50	chr12:51382000-51391400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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