Variant report

Variant	rs61730859
Chromosome Location	chr12:49579627-49579628
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	HEY1	chr12:49578738-49579751	K562	blood:	n/a	n/a
2	POLR2A	chr12:49579462-49579758	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:49578653-49579773	GM12878	blood:	n/a	n/a
4	PAX5	chr12:49579064-49579706	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:49578704-49579748	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:49578663-49579788	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:49578676-49579792	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:49578745-49579657	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:49578753-49579661	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:49578533-49579834	GM12892	blood:	n/a	n/a
11	HEY1	chr12:49578670-49579800	K562	blood:	n/a	n/a
12	POLR2A	chr12:49578680-49579818	GM12891	blood:	n/a	n/a
13	POLR2A	chr12:49578607-49579894	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:49578545-49579887	GM12878	blood:	n/a	n/a
15	REST	chr12:49579315-49585380	H1-neurons	neurons:	n/a	chr12:49581154-49581167 chr12:49581154-49581167 chr12:49581714-49581734 chr12:49582472-49582485 chr12:49581151-49581171 chr12:49580352-49580362 chr12:49581151-49581171 chr12:49580345-49580358
16	POLR2A	chr12:49576836-49579887	SK-N-SH	brain:	n/a	n/a
17	POU2F2	chr12:49578696-49579739	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:49578652-49579718	GM12891	blood:	n/a	n/a
19	POLR2A	chr12:49578722-49579790	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:49578793-49579751	A549	lung:	n/a	n/a
21	POLR2A	chr12:49578715-49579769	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr12:49578572-49579820	GM12891	blood:	n/a	n/a
23	POLR2A	chr12:49578335-49579942	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:49578586-49579795	GM12892	blood:	n/a	n/a
25	POLR2A	chr12:49578539-49579678	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr12:49578655-49579797	GM12892	blood:	n/a	n/a
27	POLR2A	chr12:49578741-49579773	Hela-S3	cervix:	n/a	n/a
28	ZBTB33	chr12:49578679-49579803	K562	blood:	n/a	n/a
29	POU2F2	chr12:49578760-49579784	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49523298..49526534-chr12:49578242..49583023,5	K562	blood:
2	chr12:49523810..49525846-chr12:49575368..49579813,5	K562	blood:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10083069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10160974	1.00[EUR][1000 genomes]
rs11168879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12299500	1.00[EUR][1000 genomes]
rs12303622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12305752	1.00[AMR][1000 genomes]
rs12308393	1.00[EUR][1000 genomes]
rs12315499	1.00[EUR][1000 genomes]
rs12317546	1.00[EUR][1000 genomes]
rs12318545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3842281	1.00[EUR][1000 genomes]
rs7342336	1.00[AMR][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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv976610	chr12:49577937-49580571	Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49570600-49581000	Weak transcription	GM12878-XiMat	blood
2	chr12:49574200-49580600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:49576000-49580800	Weak transcription	A549	lung
4	chr12:49576200-49580800	Weak transcription	Fetal Kidney	kidney
5	chr12:49576400-49580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:49576800-49581800	Weak transcription	Liver	Liver
7	chr12:49577000-49580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:49577000-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:49577200-49580200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:49577200-49580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:49577200-49581000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:49577200-49581000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:49577400-49579800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:49577400-49580000	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:49577400-49580200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:49577400-49580200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:49577400-49580400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:49577400-49580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:49577400-49580800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:49577400-49581000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:49577400-49581000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:49577400-49581000	Weak transcription	Colonic Mucosa	Colon
23	chr12:49577400-49581000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:49577400-49581800	Weak transcription	Pancreas	Pancrea
25	chr12:49577400-49581800	Weak transcription	Small Intestine	intestine
26	chr12:49577600-49579800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:49577600-49579800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:49577600-49580000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:49577600-49580000	Strong transcription	NHDF-Ad	bronchial
30	chr12:49577600-49580600	Strong transcription	Adipose Nuclei	Adipose
31	chr12:49577600-49580800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:49577600-49581000	Strong transcription	Primary T cells from cord blood	blood
33	chr12:49577600-49581000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
34	chr12:49577800-49579800	Weak transcription	Fetal Heart	heart
35	chr12:49577800-49580000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr12:49577800-49580200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:49577800-49580200	Strong transcription	Lung	lung
38	chr12:49577800-49580200	Weak transcription	HMEC	breast
39	chr12:49577800-49580200	Strong transcription	Osteobl	bone
40	chr12:49577800-49580400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:49577800-49580400	Strong transcription	Left Ventricle	heart
42	chr12:49577800-49580800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:49577800-49580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:49577800-49581000	Strong transcription	Thymus	Thymus
45	chr12:49577800-49581800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:49578000-49580000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:49578000-49580000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:49578000-49580000	Strong transcription	Fetal Stomach	stomach
49	chr12:49578000-49580200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:49578000-49580400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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