Variant report

Variant	rs12823402
Chromosome Location	chr12:51521922-51521923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51476824..51479027-chr12:51519874..51522162,2	MCF-7	breast:
2	chr12:51516030..51518469-chr12:51520883..51522469,2	K562	blood:
3	chr12:51519067..51522017-chr12:51633023..51634538,2	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1056897	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169682	0.84[EUR][1000 genomes]
rs11169712	0.88[EUR][1000 genomes]
rs11169726	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169727	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169729	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169731	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169732	0.81[AMR][1000 genomes]
rs11169736	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169742	0.84[AMR][1000 genomes]
rs11169752	0.81[AMR][1000 genomes]
rs11738	0.81[AMR][1000 genomes]
rs11831810	0.85[EUR][1000 genomes]
rs11831946	0.85[EUR][1000 genomes]
rs11833022	0.85[EUR][1000 genomes]
rs11834746	0.88[EUR][1000 genomes]
rs12370820	0.84[EUR][1000 genomes]
rs12809832	0.84[AMR][1000 genomes]
rs12810174	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12810455	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12810596	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12810700	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12811508	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12811658	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12811684	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12812650	0.85[EUR][1000 genomes]
rs12813309	0.83[EUR][1000 genomes]
rs12813368	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12814498	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12815367	0.80[ASN][1000 genomes]
rs12819225	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12819517	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12820074	0.82[EUR][1000 genomes]
rs12820559	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12820966	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12822509	0.85[EUR][1000 genomes]
rs12824225	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12826153	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12828349	0.85[EUR][1000 genomes]
rs12829630	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12833565	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17296192	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34057357	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34481246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34498074	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34735738	0.85[EUR][1000 genomes]
rs4768964	0.85[EUR][1000 genomes]
rs4768967	0.85[EUR][1000 genomes]
rs6580784	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6580792	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580793	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67260912	0.86[EUR][1000 genomes]
rs67293043	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7135059	0.84[EUR][1000 genomes]
rs7954140	0.85[EUR][1000 genomes]
rs7955251	0.80[ASN][1000 genomes]
rs7958064	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7960381	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964570	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7976777	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7977104	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7978723	0.83[EUR][1000 genomes]
rs7980874	0.84[EUR][1000 genomes]
rs970098	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs970099	0.81[AMR][1000 genomes];0.86[EUR][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:51502200-51527200	Weak transcription	Colonic Mucosa	Colon
5	chr12:51502800-51531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
7	chr12:51503600-51532000	Weak transcription	Brain Angular Gyrus	brain
8	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:51507800-51532200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:51507800-51539800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:51508000-51543000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:51510200-51526000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:51510200-51536200	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:51510200-51554400	Weak transcription	K562	blood
15	chr12:51511400-51531400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:51511400-51558800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:51512800-51535600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:51513000-51532200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
20	chr12:51513200-51522600	Weak transcription	NH-A	brain
21	chr12:51513200-51524200	Weak transcription	Fetal Brain Male	brain
22	chr12:51513200-51531600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:51513400-51527800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:51514400-51532200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:51517200-51547600	Weak transcription	Fetal Kidney	kidney
26	chr12:51517200-51554600	Weak transcription	HepG2	liver
27	chr12:51517600-51524600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:51519000-51526600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:51519000-51526600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:51519000-51529400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:51519000-51529400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:51519000-51530200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:51519000-51530400	Weak transcription	Ovary	ovary
34	chr12:51519000-51531600	Weak transcription	Adipose Nuclei	Adipose
35	chr12:51519000-51533800	Weak transcription	Gastric	stomach
36	chr12:51519000-51541000	Weak transcription	Brain Substantia Nigra	brain
37	chr12:51519000-51561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
40	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
41	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
42	chr12:51519200-51522800	Weak transcription	Brain Germinal Matrix	brain
43	chr12:51519200-51523000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:51519200-51523600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:51519200-51523600	Weak transcription	Fetal Intestine Small	intestine
46	chr12:51519200-51524400	Weak transcription	Fetal Stomach	stomach
47	chr12:51519200-51525600	Weak transcription	GM12878-XiMat	blood
48	chr12:51519200-51526400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:51519200-51526600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:51519200-51526600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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