Variant report

Variant	rs2620722
Chromosome Location	chr12:65007538-65007539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr12:65007372-65007965	GM12878	blood:	n/a	n/a
2	PAX5	chr12:65007467-65007885	GM12878	blood:	n/a	n/a
3	PAX5	chr12:65007536-65007897	GM12891	blood:	n/a	n/a
4	MXI1	chr12:65007269-65007866	GM12878	blood:	n/a	n/a
5	WRNIP1	chr12:65007408-65007819	GM12878	blood:	n/a	n/a
6	ATF2	chr12:65007506-65007916	GM12878	blood:	n/a	n/a
7	MTA3	chr12:65007476-65008003	GM12878	blood:	n/a	n/a
8	PAX5	chr12:65007483-65007849	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:65007515-65007949	GM12878	blood:	n/a	n/a
10	PAX5	chr12:65007415-65007986	GM12878	blood:	n/a	n/a
11	NFATC1	chr12:65007529-65007945	GM12878	blood:	n/a	n/a
12	CREB1	chr12:65007501-65007939	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:64913800..64915930-chr12:65005783..65007721,2	K562	blood:
2	chr12:65006929..65009756-chr12:65024584..65028826,3	MCF-7	breast:
3	chr12:65001130..65003993-chr12:65004405..65007719,4	K562	blood:
4	chr12:65001526..65007900-chr12:65015799..65021807,8	K562	blood:
5	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256670	TF binding region
ENSG00000225195	Chromatin interaction
ENSG00000207546	Chromatin interaction
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11175485	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175486	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175488	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175489	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175490	1.00[ASN][1000 genomes]
rs11175492	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175495	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175498	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175499	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175500	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175501	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175502	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175514	0.86[AMR][1000 genomes]
rs12367950	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368712	0.86[AMR][1000 genomes]
rs12368761	0.86[AMR][1000 genomes]
rs1795616	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56093753	0.86[AMR][1000 genomes]
rs7135985	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296498	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73321721	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73321733	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1048199	chr12:64951666-65021700	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv541512	chr12:64951666-65021700	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65002600-65007800	Active TSS	GM12878-XiMat	blood
2	chr12:65003000-65007600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:65003200-65007600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:65003400-65007600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:65005400-65007800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr12:65005600-65010200	Weak transcription	Spleen	Spleen
7	chr12:65005800-65008000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:65005800-65010200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:65005800-65015200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:65005800-65017800	Weak transcription	Gastric	stomach
11	chr12:65006000-65009800	Weak transcription	Brain Angular Gyrus	brain
12	chr12:65006000-65010000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:65006000-65012800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:65006200-65007600	Enhancers	Adipose Nuclei	Adipose
15	chr12:65006200-65007600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:65006200-65007800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:65006200-65008600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:65006200-65008800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:65006200-65009600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:65006200-65009600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:65006200-65009600	Weak transcription	HSMMtube	muscle
22	chr12:65006200-65009600	Weak transcription	Osteobl	bone
23	chr12:65006200-65009800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:65006200-65009800	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:65006200-65009800	Weak transcription	HSMM	muscle
26	chr12:65006200-65009800	Weak transcription	NHDF-Ad	bronchial
27	chr12:65006200-65010000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:65006200-65010000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:65006200-65010200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:65006200-65010200	Weak transcription	Brain Anterior Caudate	brain
31	chr12:65006200-65010200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:65006200-65013000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:65006200-65017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:65006200-65017600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:65006200-65018800	Weak transcription	Fetal Thymus	thymus
36	chr12:65006200-65019000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:65006200-65019000	Weak transcription	NHEK	skin
38	chr12:65006200-65019400	Weak transcription	Psoas Muscle	Psoas
39	chr12:65006400-65007600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:65006400-65007600	Enhancers	NHLF	lung
41	chr12:65006400-65009200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:65006400-65010200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:65006400-65010200	Weak transcription	Colonic Mucosa	Colon
44	chr12:65006400-65017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:65006600-65007600	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr12:65006600-65007600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr12:65006600-65008000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:65006600-65008800	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:65006600-65009400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr12:65006600-65009600	Weak transcription	Left Ventricle	heart

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