Variant report

Variant	rs17125227
Chromosome Location	chr12:51406388-51406389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:51406300-51406497	K562	blood:	n/a	chr12:51406443-51406457

No.	Distal block	Cell Line	Cell type
1	chr12:51405834..51407705-chr12:51409196..51411163,3	K562	blood:
2	chr12:51397497..51399942-chr12:51404608..51407015,3	MCF-7	breast:
3	chr12:51157683..51159798-chr12:51405816..51407695,2	MCF-7	breast:
4	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
5	chr12:51397539..51404278-chr12:51405080..51409503,9	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11169614	1.00[AMR][1000 genomes]
rs11169724	0.93[YRI][hapmap]
rs11835513	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12369066	0.93[YRI][hapmap]
rs17124979	1.00[AMR][1000 genomes]
rs17125085	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125212	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125245	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125367	0.92[YRI][hapmap]
rs17125370	0.93[YRI][hapmap]
rs17125418	0.93[YRI][hapmap]
rs4768973	0.93[YRI][hapmap]
rs56809906	1.00[AMR][1000 genomes]
rs56840343	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56883422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56979742	1.00[AMR][1000 genomes]
rs58343549	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58493263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60089061	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60610335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60720958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60886362	0.96[AFR][1000 genomes]
rs61550892	1.00[AMR][1000 genomes]
rs7137990	1.00[AMR][1000 genomes]
rs7303962	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs7309789	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7312269	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296205	1.00[AMR][1000 genomes]
rs73297927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297940	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297966	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298000	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308073	1.00[AMR][1000 genomes]
rs73308091	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308094	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308096	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310009	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310019	0.88[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: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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:51388600-51406600	Weak transcription	Small Intestine	intestine
4	chr12:51399200-51418000	Weak transcription	Gastric	stomach
5	chr12:51399400-51408200	Weak transcription	NHDF-Ad	bronchial
6	chr12:51399800-51406800	Weak transcription	A549	lung
7	chr12:51399800-51414600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
9	chr12:51400000-51407200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:51400000-51407400	Weak transcription	HMEC	breast
11	chr12:51401000-51410800	Weak transcription	HepG2	liver
12	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:51401600-51410000	Weak transcription	Pancreas	Pancrea
14	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
16	chr12:51402400-51406400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:51402400-51407200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:51402400-51407200	Weak transcription	Lung	lung
19	chr12:51402400-51408600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
21	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
23	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:51402600-51406400	Enhancers	Fetal Brain Male	brain
25	chr12:51402600-51406800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:51403000-51406600	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:51403000-51406600	Weak transcription	Placenta	Placenta
28	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:51403200-51407600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:51403400-51407600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:51403600-51406600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:51403600-51406600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:51403600-51406600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:51403600-51406800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:51403600-51407000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:51403600-51407400	Enhancers	Brain Hippocampus Middle	brain
39	chr12:51403600-51407600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:51403600-51410200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:51403600-51412000	Weak transcription	Fetal Intestine Small	intestine
42	chr12:51403600-51414200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:51403600-51414400	Weak transcription	Hela-S3	cervix
44	chr12:51403600-51414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:51403600-51417600	Weak transcription	HSMM	muscle
47	chr12:51403800-51406600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:51403800-51406800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:51403800-51406800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:51403800-51411200	Weak transcription	Fetal Intestine Large	intestine

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