Variant report

Variant	rs224573
Chromosome Location	chr12:51417261-51417262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
3	chr12:51381999..51383728-chr12:51415428..51417446,2	MCF-7	breast:
4	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
5	chr12:51158188..51159927-chr12:51415849..51417938,2	K562	blood:
6	chr12:51393084..51395626-chr12:51414543..51417529,2	MCF-7	breast:
7	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
8	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000272028	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

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];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10876126	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.95[AMR][1000 genomes]
rs11169679	0.86[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]
rs12423207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814178	0.85[AFR][1000 genomes]
rs150909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs161044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][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]
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[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs17125416	1.00[JPT][hapmap]
rs17125418	1.00[JPT][hapmap]
rs17125428	1.00[JPT][hapmap]
rs17229232	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	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]
rs224569	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]
rs224570	1.00[JPT][hapmap];0.91[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][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	0.88[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	1.00[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]
rs2630353	0.83[AMR][1000 genomes]
rs2630358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][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]
rs2630366	1.00[AMR][1000 genomes]
rs2630367	1.00[AMR][1000 genomes]
rs319930	1.00[AMR][1000 genomes]
rs319938	1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs319944	0.83[AMR][1000 genomes]
rs364627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[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];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768959	0.89[ASW][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768967	0.81[YRI][hapmap]
rs4768973	1.00[JPT][hapmap]
rs55874852	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.92[EUR][1000 genomes]
rs6580779	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6580783	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs686528	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7299484	0.94[AFR][1000 genomes];0.94[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	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.92[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[ASW][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7975628	1.00[ASW][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs829016	0.83[AMR][1000 genomes]
rs829021	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs224573	SLC11A2	cis	multi-tissue	Pritchard
rs224573	SLC11A2	cis	lymphoblastoid	seeQTL
rs224573	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
5	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
6	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:51403600-51417600	Weak transcription	HSMM	muscle
11	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
12	chr12:51406400-51417400	Weak transcription	Osteobl	bone
13	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:51407600-51417600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:51409000-51417400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
20	chr12:51412200-51417800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:51412800-51417800	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:51412800-51418000	Enhancers	Primary T cells from cord blood	blood
24	chr12:51413000-51417600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:51413200-51418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr12:51413800-51418000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:51414000-51417600	Enhancers	HepG2	liver
28	chr12:51414400-51417400	Enhancers	Liver	Liver
29	chr12:51414400-51418000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr12:51414600-51417400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:51414800-51417400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:51415000-51417400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:51415000-51417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:51415200-51417600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:51415200-51417600	Enhancers	Fetal Intestine Large	intestine
36	chr12:51415400-51417600	Enhancers	Fetal Intestine Small	intestine
37	chr12:51415400-51418200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:51415800-51417400	Enhancers	Hela-S3	cervix
39	chr12:51415800-51417600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:51415800-51417800	Enhancers	Duodenum Mucosa	Duodenum
41	chr12:51416000-51417400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:51416000-51417400	Weak transcription	Brain Anterior Caudate	brain
43	chr12:51416000-51417400	Enhancers	Brain Hippocampus Middle	brain
44	chr12:51416000-51417400	Weak transcription	Fetal Lung	lung
45	chr12:51416000-51417400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:51416000-51417600	Enhancers	Thymus	Thymus
47	chr12:51416000-51417800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:51416000-51417800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:51416000-51417800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:51416000-51418000	Weak transcription	Primary B cells from peripheral blood	blood

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