Variant report

Variant	rs452587
Chromosome Location	chr12:51415047-51415048
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51404293..51409685-chr12:51411834..51415817,7	K562	blood:
2	chr12:51399342..51401047-chr12:51411160..51415071,3	MCF-7	breast:
3	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
4	chr12:51400476..51402543-chr12:51413177..51415627,2	K562	blood:
5	chr12:51381778..51384453-chr12:51414411..51415934,2	MCF-7	breast:
6	chr12:51155647..51158511-chr12:51413575..51415809,2	K562	blood:
7	chr12:51393084..51395626-chr12:51414543..51417529,2	MCF-7	breast:
8	chr12:51386892..51388716-chr12:51412820..51415080,2	K562	blood:
9	chr12:51412418..51415100-chr12:51610730..51614429,3	K562	blood:
10	chr12:51413146..51415760-chr12:51440931..51443529,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184271	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000272028	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1026994	1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10783412	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]
rs12423207	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814178	0.81[AFR][1000 genomes]
rs150909	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229232	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029147	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046498	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs224586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.90[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]
rs2630353	0.83[AMR][1000 genomes]
rs2630358	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	0.93[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[AMR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.83[AMR][1000 genomes]
rs319944	0.83[AMR][1000 genomes]
rs364627	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	0.98[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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768959	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55874852	0.85[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	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	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	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs686528	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7299484	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968372	0.80[EUR][1000 genomes]
rs7969536	0.87[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	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.86[AMR][1000 genomes]
rs7975628	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs829016	0.83[AMR][1000 genomes]
rs829021	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs452587	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
3	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
6	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
7	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
9	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:51403600-51417600	Weak transcription	HSMM	muscle
15	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
16	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
17	chr12:51406000-51415200	Weak transcription	Right Atrium	heart
18	chr12:51406400-51417200	Weak transcription	Fetal Brain Male	brain
19	chr12:51406400-51417400	Weak transcription	Osteobl	bone
20	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:51407200-51415800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:51407400-51415200	Weak transcription	Placenta	Placenta
26	chr12:51407600-51415200	Weak transcription	Lung	lung
27	chr12:51407600-51415600	Weak transcription	Small Intestine	intestine
28	chr12:51407600-51417200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:51407600-51417600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:51408600-51417000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:51408600-51417000	Weak transcription	Psoas Muscle	Psoas
32	chr12:51409000-51417400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:51409800-51416400	Weak transcription	Fetal Kidney	kidney
34	chr12:51410400-51415200	Weak transcription	Pancreas	Pancrea
35	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
36	chr12:51411800-51415600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:51411800-51416400	Weak transcription	A549	lung
38	chr12:51412200-51417800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:51412400-51415600	Enhancers	Brain Hippocampus Middle	brain
40	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
41	chr12:51412800-51415400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:51412800-51415400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:51412800-51416200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:51412800-51416600	Enhancers	Brain Substantia Nigra	brain
45	chr12:51412800-51417800	Enhancers	Brain Cingulate Gyrus	brain
46	chr12:51412800-51418000	Enhancers	Primary T cells from cord blood	blood
47	chr12:51413000-51417200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:51413000-51417600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:51413200-51418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:51413400-51416200	Enhancers	Brain Angular Gyrus	brain

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