Variant report

Variant	rs319943
Chromosome Location	chr12:51328163-51328164
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51320296..51325528-chr12:51326081..51329757,6	K562	blood:
2	chr12:51155577..51158577-chr12:51327388..51330247,3	MCF-7	breast:
3	chr12:51325095..51328187-chr12:51330132..51332748,3	K562	blood:
4	chr12:51233571..51235108-chr12:51328091..51331063,2	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12423207	0.82[CEU][hapmap]
rs150909	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161044	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161045	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161046	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161047	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2046498	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs224564	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224566	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224569	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224570	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224573	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs224574	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs224578	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs224585	0.80[EUR][1000 genomes]
rs224586	0.83[AMR][1000 genomes]
rs224590	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs224592	0.82[EUR][1000 genomes]
rs224593	0.82[EUR][1000 genomes]
rs2554858	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554859	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630353	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630358	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2630362	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630366	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630367	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs319930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319938	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319940	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319941	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319944	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364627	0.82[CEU][hapmap]
rs390424	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs394384	0.82[CEU][hapmap]
rs445520	0.82[EUR][1000 genomes]
rs452587	0.83[AMR][1000 genomes]
rs4768875	0.83[AMR][1000 genomes]
rs55874852	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580779	0.82[CEU][hapmap]
rs6580780	0.82[CEU][hapmap]
rs706803	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs706804	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7138860	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829021	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs853236	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs861204	1.00[JPT][hapmap]

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
rs319943	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51320200-51330600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:51320400-51328600	Weak transcription	HSMM	muscle
4	chr12:51320600-51328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:51322200-51332600	Weak transcription	Fetal Kidney	kidney
6	chr12:51322400-51329000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:51322800-51328200	Weak transcription	NHEK	skin
8	chr12:51322800-51331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:51323000-51331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
11	chr12:51323400-51330000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:51323400-51330800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:51323400-51330800	Weak transcription	Brain Germinal Matrix	brain
14	chr12:51323400-51330800	Weak transcription	Fetal Brain Female	brain
15	chr12:51323600-51328200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:51323600-51328400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:51324200-51331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:51324400-51331200	Enhancers	Stomach Mucosa	stomach
19	chr12:51324600-51331000	Weak transcription	Lung	lung
20	chr12:51324800-51328200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:51325000-51329800	Enhancers	Fetal Intestine Small	intestine
22	chr12:51325200-51328800	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr12:51325400-51331000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:51325600-51328400	Genic enhancers	Primary B cells from cord blood	blood
25	chr12:51325600-51328400	Enhancers	Small Intestine	intestine
26	chr12:51325800-51328200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:51325800-51328400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr12:51326000-51328200	Genic enhancers	Adipose Nuclei	Adipose
29	chr12:51326200-51329600	Enhancers	Colon Smooth Muscle	Colon
30	chr12:51326400-51328400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:51326400-51328600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:51326400-51329600	Enhancers	Hela-S3	cervix
33	chr12:51326400-51331000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:51326600-51328200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:51326600-51328800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:51326600-51329400	Enhancers	HMEC	breast
37	chr12:51326600-51329600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:51326800-51329800	Enhancers	Fetal Intestine Large	intestine
39	chr12:51327200-51328200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:51327200-51328200	Enhancers	Right Atrium	heart
41	chr12:51327200-51328400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:51327200-51328400	Enhancers	Psoas Muscle	Psoas
43	chr12:51327200-51328600	Enhancers	NHDF-Ad	bronchial
44	chr12:51327200-51329400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:51327200-51330800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:51327200-51331400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr12:51327400-51328200	Enhancers	Primary hematopoietic stem cells	blood
48	chr12:51327400-51328200	Weak transcription	Ovary	ovary
49	chr12:51327400-51328400	Enhancers	Gastric	stomach
50	chr12:51327400-51328600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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