Variant report

Variant	rs60089061
Chromosome Location	chr12:51447695-51447696
allele	A/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	POLR2A	chr12:51447602-51447714	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51446371..51449109-chr12:51475954..51477544,3	K562	blood:
2	chr12:51446671..51449109-chr12:51475852..51477454,2	K562	blood:
3	chr12:51445541..51448064-chr12:51474329..51477358,3	MCF-7	breast:
4	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11169614	1.00[AMR][1000 genomes]
rs11835513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125085	1.00[AMR][1000 genomes]
rs17125212	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56809906	1.00[AMR][1000 genomes]
rs56840343	1.00[AMR][1000 genomes]
rs56883422	1.00[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60610335	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60720958	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60886362	0.92[AFR][1000 genomes]
rs61550892	1.00[AMR][1000 genomes]
rs7137990	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7303962	1.00[AMR][1000 genomes]
rs7309789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7312269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296205	1.00[AMR][1000 genomes]
rs73297927	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297940	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300041	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308073	1.00[AMR][1000 genomes]
rs73308091	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308094	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308096	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310019	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310024	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51442800-51449000	Weak transcription	Aorta	Aorta
3	chr12:51442800-51449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:51442800-51450000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:51442800-51452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:51443000-51448200	Weak transcription	Gastric	stomach
8	chr12:51443000-51453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:51443200-51449600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:51443400-51448200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:51443400-51448200	Weak transcription	Esophagus	oesophagus
12	chr12:51443400-51449200	Weak transcription	Right Ventricle	heart
13	chr12:51443400-51452600	Weak transcription	Stomach Mucosa	stomach
14	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:51443600-51447800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:51443600-51448600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:51443600-51451600	Weak transcription	Colonic Mucosa	Colon
18	chr12:51443600-51451800	Weak transcription	Small Intestine	intestine
19	chr12:51443600-51452600	Weak transcription	Psoas Muscle	Psoas
20	chr12:51443600-51457400	Weak transcription	Fetal Brain Male	brain
21	chr12:51443600-51459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:51443600-51462800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:51443800-51447800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:51443800-51448000	Weak transcription	NHLF	lung
25	chr12:51443800-51449000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:51443800-51455600	Weak transcription	Fetal Heart	heart
27	chr12:51443800-51462600	Strong transcription	A549	lung
28	chr12:51444000-51449600	Weak transcription	HUVEC	blood vessel
29	chr12:51444200-51448200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:51444200-51452400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:51444200-51454800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:51444200-51463200	Strong transcription	Placenta	Placenta
33	chr12:51444200-51465000	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:51444200-51465400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:51444200-51465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
37	chr12:51444400-51462800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:51444400-51464800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:51444600-51455600	Strong transcription	Fetal Intestine Small	intestine
40	chr12:51445000-51467800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:51445400-51449600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:51445400-51449800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:51445400-51449800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:51445400-51454000	Strong transcription	Left Ventricle	heart
45	chr12:51445400-51462600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr12:51445400-51462600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:51445400-51462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:51445400-51462800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:51445400-51464000	Strong transcription	Fetal Intestine Large	intestine
50	chr12:51445400-51467800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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