Variant report

Variant	rs224576
Chromosome Location	chr12:51420899-51420900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51418173-51421529	HepG2	liver:	n/a	n/a
2	HEY1	chr12:51420837-51421268	HepG2	liver:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51393339..51395355-chr12:51418733..51421410,2	MCF-7	breast:
2	chr12:51385408..51389476-chr12:51420028..51421870,3	MCF-7	breast:
3	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
4	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
5	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
6	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
7	chr12:51418513..51423622-chr12:51474378..51479071,10	MCF-7	breast:
8	chr12:51419815..51423306-chr17:56706440..56710556,3	MCF-7	breast:
9	chr12:51419463..51422870-chr12:51476162..51478400,3	K562	blood:
10	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
11	chr12:51156017..51159008-chr12:51420473..51422056,2	MCF-7	breast:
12	chr12:51377924..51379984-chr12:51420251..51421770,2	MCF-7	breast:
13	chr12:51388022..51389545-chr12:51419948..51422038,2	MCF-7	breast:
14	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
15	chr12:51419952..51421943-chr12:51475612..51477490,4	K562	blood:
16	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
17	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
18	chr12:51316948..51319607-chr12:51419309..51421732,3	K562	blood:
19	chr12:51420182..51422992-chr12:51631104..51633893,3	MCF-7	breast:
20	chr12:51316948..51319607-chr12:51419309..51421732,2	K562	blood:
21	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

No data

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000185432	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026994	0.83[ASN][1000 genomes]
rs10747603	0.83[ASN][1000 genomes]
rs10783411	0.83[ASN][1000 genomes]
rs10783412	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10876126	0.83[ASN][1000 genomes]
rs11169679	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12423207	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12814178	0.85[AFR][1000 genomes]
rs150909	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs161044	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs161045	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161046	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161047	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17229232	0.83[ASN][1000 genomes]
rs2029147	0.83[ASN][1000 genomes]
rs224564	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224566	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224569	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224570	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224573	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224574	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224585	0.95[AFR][1000 genomes]
rs224586	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs224590	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs224592	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224593	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2630358	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2630362	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2630366	0.82[AMR][1000 genomes]
rs2630367	0.82[AMR][1000 genomes]
rs319930	0.82[AMR][1000 genomes]
rs319938	0.82[AMR][1000 genomes]
rs364627	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs390424	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs394384	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs416062	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4238110	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs435965	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs445520	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs452587	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768875	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768959	0.83[ASN][1000 genomes]
rs55874852	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58309379	0.83[ASN][1000 genomes]
rs613977	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580779	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6580780	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580783	0.83[ASN][1000 genomes]
rs686528	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs706803	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7299484	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969536	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7971712	0.83[ASN][1000 genomes]
rs7972608	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7974923	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7975117	0.82[AFR][1000 genomes]
rs7975628	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7977993	0.83[ASN][1000 genomes]
rs829021	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs853236	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9739943	0.86[AFR][1000 genomes];0.83[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
rs224576	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51418200-51421200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:51420200-51421400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:51420200-51422400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:51420200-51423000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:51420400-51421400	Enhancers	Fetal Heart	heart
6	chr12:51420400-51422000	Flanking Active TSS	HepG2	liver
7	chr12:51420600-51421000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:51420600-51421000	Enhancers	Primary B cells from cord blood	blood
9	chr12:51420600-51421000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:51420600-51421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:51420600-51421200	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:51420600-51421200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr12:51420600-51421200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:51420600-51421200	Enhancers	Fetal Intestine Small	intestine
15	chr12:51420600-51421200	Enhancers	Spleen	Spleen
16	chr12:51420600-51421200	Enhancers	Hela-S3	cervix
17	chr12:51420600-51421400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:51420600-51421400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:51420600-51421400	Enhancers	Fetal Intestine Large	intestine
20	chr12:51420600-51421400	Enhancers	Pancreas	Pancrea
21	chr12:51420600-51421400	Weak transcription	A549	lung
22	chr12:51420600-51421600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:51420600-51421600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:51420600-51421600	Weak transcription	NHEK	skin
25	chr12:51420600-51421800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:51420600-51421800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:51420600-51421800	Weak transcription	Stomach Mucosa	stomach
28	chr12:51420600-51422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:51420600-51422000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:51420600-51422000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:51420600-51422000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr12:51420600-51422000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:51420600-51422000	Weak transcription	Osteobl	bone
34	chr12:51420600-51422200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:51420600-51422200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:51420600-51422200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:51420600-51422200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr12:51420600-51422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:51420600-51422200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:51420600-51422200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:51420600-51422200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:51420600-51422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:51420600-51422200	Weak transcription	Liver	Liver
44	chr12:51420600-51422200	Enhancers	HMEC	breast
45	chr12:51420600-51422400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:51420600-51422400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:51420600-51422400	Weak transcription	Fetal Kidney	kidney
48	chr12:51420600-51422400	Enhancers	Placenta	Placenta
49	chr12:51420600-51422600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:51420600-51422600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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