Variant report

Variant	rs12424860
Chromosome Location	chr12:51159140-51159141
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50497524..50499290-chr12:51157685..51160627,2	MCF-7	breast:
2	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
3	chr12:50793597..50795392-chr12:51156771..51159161,2	MCF-7	breast:
4	chr12:51157036..51159803-chr12:51442013..51443781,2	K562	blood:
5	chr12:51159003..51159746-chr12:51745461..51746336,2	K562	blood:
6	chr12:51158475..51160420-chr12:51281763..51283394,2	K562	blood:
7	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
8	chr12:51158682..51159758-chr12:51380494..51381376,3	MCF-7	breast:
9	chr12:50898290..50900177-chr12:51158500..51160466,2	MCF-7	breast:
10	chr12:51155753..51160968-chr12:51475872..51478809,5	MCF-7	breast:
11	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
12	chr12:51156583..51159237-chr12:51477140..51478642,2	MCF-7	breast:
13	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
14	chr12:51157529..51159205-chr6:26158256..26159760,2	MCF-7	breast:
15	chr12:51158399..51160694-chr12:51565412..51567742,2	K562	blood:
16	chr12:51155941..51160401-chr12:51475746..51478915,6	K562	blood:
17	chr12:50897453..50902823-chr12:51156009..51160960,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000050426	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10459235	0.90[ASN][1000 genomes]
rs10506294	0.80[AMR][1000 genomes]
rs10747587	0.82[AMR][1000 genomes]
rs10783382	0.80[ASN][1000 genomes]
rs10783383	0.81[AMR][1000 genomes]
rs10783384	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783389	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876080	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876089	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876090	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876094	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876095	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876096	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876097	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169528	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169532	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11169537	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11169538	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169539	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169544	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169560	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169561	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11615933	0.88[ASN][1000 genomes]
rs12580479	0.84[ASN][1000 genomes]
rs12809086	0.80[AMR][1000 genomes]
rs1344958	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17124930	0.81[AMR][1000 genomes]
rs35845404	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3742063	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3742064	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3809319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825402	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4026593	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238108	0.80[AMR][1000 genomes]
rs4307773	0.94[ASN][1000 genomes]
rs4768866	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768906	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4768907	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768911	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768912	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768913	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768914	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768917	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768921	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768922	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768923	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768924	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768925	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768940	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73094900	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73096846	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12424860	DIP2B	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51155600-51159600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:51155800-51159400	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr12:51156000-51159200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:51156000-51159200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:51156000-51159200	Active TSS	Left Ventricle	heart
6	chr12:51156000-51159600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:51156000-51159600	Active TSS	Colonic Mucosa	Colon
8	chr12:51156000-51159600	Active TSS	Right Ventricle	heart
9	chr12:51156000-51159600	Active TSS	K562	blood
10	chr12:51156200-51159200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:51156200-51159400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr12:51156200-51159400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:51156200-51159400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:51156200-51159400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:51156200-51159400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr12:51156200-51159400	Active TSS	Placenta	Placenta
17	chr12:51156200-51159400	Active TSS	Psoas Muscle	Psoas
18	chr12:51156200-51159600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:51156200-51159800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:51156200-51160000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:51156400-51159200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:51156400-51159200	Active TSS	HepG2	liver
23	chr12:51156400-51159400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:51156400-51159400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:51156400-51159800	Active TSS	Rectal Smooth Muscle	rectum
26	chr12:51156600-51159200	Active TSS	A549	lung
27	chr12:51156600-51159400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:51156600-51159400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:51156600-51159400	Active TSS	Fetal Stomach	stomach
30	chr12:51156600-51159400	Active TSS	HSMM	muscle
31	chr12:51156600-51159600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:51156600-51159600	Active TSS	Fetal Brain Female	brain
33	chr12:51156800-51159200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:51156800-51159200	Active TSS	Stomach Mucosa	stomach
35	chr12:51156800-51159400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:51156800-51159400	Active TSS	Brain Angular Gyrus	brain
37	chr12:51156800-51159400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:51156800-51159400	Active TSS	GM12878-XiMat	blood
39	chr12:51156800-51159400	Active TSS	Hela-S3	cervix
40	chr12:51156800-51159600	Active TSS	NHDF-Ad	bronchial
41	chr12:51156800-51159600	Active TSS	NHLF	lung
42	chr12:51157000-51159200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:51157000-51159200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:51157000-51159200	Active TSS	Aorta	Aorta
45	chr12:51157000-51159200	Active TSS	Lung	lung
46	chr12:51157000-51159200	Active TSS	Ovary	ovary
47	chr12:51157000-51159600	Active TSS	Thymus	Thymus
48	chr12:51157200-51159200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:51157200-51159200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr12:51157200-51159200	Active TSS	Colon Smooth Muscle	Colon

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