Variant report

Variant	rs17125085
Chromosome Location	chr12:51326429-51326430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51325611..51327602-chr12:51338374..51340609,2	K562	blood:
2	chr12:51322696..51325064-chr12:51325952..51327620,2	K562	blood:
3	chr12:51325288..51327339-chr12:51334095..51336282,2	K562	blood:
4	chr12:51325095..51327824-chr12:51330132..51332828,3	K562	blood:
5	chr12:51320296..51325528-chr12:51326081..51329757,6	K562	blood:
6	chr12:51325095..51328187-chr12:51330132..51332748,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11169614	1.00[AMR][1000 genomes]
rs11835513	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17124979	1.00[AMR][1000 genomes]
rs17125212	0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125227	0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125245	0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125367	0.84[YRI][hapmap]
rs17125370	0.86[YRI][hapmap]
rs56809906	1.00[AMR][1000 genomes]
rs56840343	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56883422	1.00[AMR][1000 genomes]
rs56979742	1.00[AMR][1000 genomes]
rs58343549	1.00[AMR][1000 genomes]
rs58493263	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60089061	1.00[AMR][1000 genomes]
rs60610335	1.00[AMR][1000 genomes]
rs60720958	1.00[AMR][1000 genomes]
rs60886362	0.85[AFR][1000 genomes]
rs61550892	1.00[AMR][1000 genomes]
rs7137990	1.00[AMR][1000 genomes]
rs7303962	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs7309789	1.00[AMR][1000 genomes]
rs7312269	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296205	1.00[AMR][1000 genomes]
rs73297927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297940	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297966	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298000	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300041	1.00[AMR][1000 genomes]
rs73308073	1.00[AMR][1000 genomes]
rs73308091	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308094	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310009	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310024	1.00[AMR][1000 genomes]
rs73311230	1.00[AMR][1000 genomes]
rs73311252	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17125085	SLC11A2	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr12:51320600-51327400	Weak transcription	Placenta	Placenta
5	chr12:51320600-51328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51322200-51326600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51322200-51327200	Weak transcription	Fetal Heart	heart
8	chr12:51322200-51327200	Weak transcription	NHDF-Ad	bronchial
9	chr12:51322200-51327400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:51322200-51327400	Weak transcription	HSMMtube	muscle
11	chr12:51322200-51332600	Weak transcription	Fetal Kidney	kidney
12	chr12:51322400-51327200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:51322400-51327200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:51322400-51327200	Weak transcription	Esophagus	oesophagus
15	chr12:51322400-51327600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:51322400-51327800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:51322400-51329000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:51322600-51326600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:51322600-51326600	Weak transcription	HMEC	breast
20	chr12:51322600-51326800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:51322600-51327200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:51322800-51326800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:51322800-51327600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:51322800-51328200	Weak transcription	NHEK	skin
25	chr12:51322800-51331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:51323000-51327200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:51323000-51327200	Weak transcription	Right Atrium	heart
28	chr12:51323000-51327800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:51323000-51331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
31	chr12:51323200-51328000	Weak transcription	NHLF	lung
32	chr12:51323400-51327200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:51323400-51327200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:51323400-51327600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:51323400-51327600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:51323400-51330000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:51323400-51330800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:51323400-51330800	Weak transcription	Brain Germinal Matrix	brain
39	chr12:51323400-51330800	Weak transcription	Fetal Brain Female	brain
40	chr12:51323600-51326600	Weak transcription	Brain Substantia Nigra	brain
41	chr12:51323600-51326600	Weak transcription	Dnd41	blood
42	chr12:51323600-51327200	Weak transcription	Brain Anterior Caudate	brain
43	chr12:51323600-51328200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:51323600-51328400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:51323800-51326600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:51323800-51328000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr12:51324000-51328000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:51324200-51331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:51324400-51326600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:51324400-51331200	Enhancers	Stomach Mucosa	stomach

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