Variant report

Variant	rs59576871
Chromosome Location	chr12:50034992-50034993
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50034654-50035072	GM12878	blood:	n/a	n/a
2	STAT5A	chr12:50034564-50035076	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:50034632-50035072	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:50033775-50036287	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:50034491-50035207	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:50034465-50035293	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:50034589-50035835	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:50032890-50036362	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:50033740-50035234	HUVEC	blood vessel:	n/a	n/a
10	NFATC1	chr12:50034290-50035200	GM12878	blood:	n/a	n/a
11	PML	chr12:50033621-50035892	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:50034822-50035078	U87	brain:	n/a	n/a
13	NFATC1	chr12:50034513-50035225	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:50034722-50035137	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:50034502-50035369	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:50034584-50035210	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:50034747-50035044	K562	blood:	n/a	n/a
18	POLR2A	chr12:50034636-50035071	H1-hESC	embryonic stem cell:	n/a	n/a
19	MTA3	chr12:50034476-50035160	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:50034918-50035107	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:50028209-50038752	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:50033620-50036847	K562	blood:	n/a	n/a
23	POLR2A	chr12:50033709-50035218	GM12878	blood:	n/a	n/a
24	BCL3	chr12:50034674-50035819	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:50034737-50035082	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50026061..50028133-chr12:50034588..50036423,2	MCF-7	breast:
2	chr12:50032692..50036397-chr12:50134121..50137732,4	K562	blood:
3	chr12:50033388..50039946-chr12:50098324..50104633,12	K562	blood:
4	chr12:50034899..50039875-chr12:50099580..50104040,10	MCF-7	breast:
5	chr12:50029309..50033089-chr12:50034924..50039284,4	MCF-7	breast:
6	chr12:50033000..50035088-chr12:50036233..50037889,2	K562	blood:
7	chr12:50034262..50036301-chr12:50135130..50136792,2	MCF-7	breast:
8	chr12:50034792..50037602-chr12:50234677..50237742,4	MCF-7	breast:
9	chr12:50034825..50036766-chr12:50235780..50238026,2	MCF-7	breast:
10	chr12:50014216..50017582-chr12:50033050..50038779,6	MCF-7	breast:
11	chr12:50032076..50035986-chr12:50043238..50048000,4	MCF-7	breast:
12	chr12:50024342..50028618-chr12:50029311..50035232,8	K562	blood:
13	chr12:50034541..50040504-chr12:50134095..50137099,9	MCF-7	breast:

No data

Variant related genes	Relation type
PRPF40B	TF binding region
FMNL3	TF binding region
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000257570	Chromatin interaction
ENSG00000186666	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11169071	1.00[EUR][1000 genomes]
rs11830472	0.83[AFR][1000 genomes]
rs11831670	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11831673	0.83[AFR][1000 genomes]
rs11831877	0.86[AFR][1000 genomes]
rs11832727	0.91[AFR][1000 genomes]
rs11835085	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11837399	0.91[AFR][1000 genomes]
rs11837408	0.91[AFR][1000 genomes]
rs11837637	0.94[AFR][1000 genomes]
rs12298123	1.00[EUR][1000 genomes]
rs12299477	1.00[EUR][1000 genomes]
rs12299743	1.00[EUR][1000 genomes]
rs12300085	1.00[EUR][1000 genomes]
rs12306942	1.00[EUR][1000 genomes]
rs12309399	1.00[EUR][1000 genomes]
rs12311319	1.00[EUR][1000 genomes]
rs12311910	1.00[EUR][1000 genomes]
rs12313583	1.00[EUR][1000 genomes]
rs12314348	1.00[EUR][1000 genomes]
rs12315746	1.00[EUR][1000 genomes]
rs12315941	1.00[EUR][1000 genomes]
rs12319527	1.00[EUR][1000 genomes]
rs12320104	1.00[EUR][1000 genomes]
rs12320612	1.00[EUR][1000 genomes]
rs12321717	1.00[EUR][1000 genomes]
rs28420769	1.00[EUR][1000 genomes]
rs57970210	1.00[EUR][1000 genomes]
rs58072420	0.97[AFR][1000 genomes]
rs58867453	1.00[EUR][1000 genomes]
rs59570650	1.00[EUR][1000 genomes]
rs59597892	0.91[AFR][1000 genomes]
rs60117004	0.86[AFR][1000 genomes]
rs60507124	1.00[EUR][1000 genomes]
rs61227990	1.00[EUR][1000 genomes]
rs7131756	0.86[AFR][1000 genomes]
rs7134329	0.91[AFR][1000 genomes]
rs7307183	0.91[AFR][1000 genomes]
rs7312037	0.86[AFR][1000 genomes]
rs7313183	0.86[AFR][1000 genomes]
rs7313590	0.86[AFR][1000 genomes]
rs7960185	1.00[EUR][1000 genomes]
rs7978381	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50017600-50035600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:50017800-50036400	Weak transcription	Colonic Mucosa	Colon
3	chr12:50017800-50042200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:50018000-50035400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:50018000-50035600	Weak transcription	Left Ventricle	heart
6	chr12:50018000-50035800	Weak transcription	HSMMtube	muscle
7	chr12:50018000-50043000	Weak transcription	Psoas Muscle	Psoas
8	chr12:50019000-50038200	Weak transcription	K562	blood
9	chr12:50022000-50036600	Weak transcription	NHDF-Ad	bronchial
10	chr12:50024600-50036400	Weak transcription	Thymus	Thymus
11	chr12:50024800-50035400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:50025200-50035200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:50028400-50035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:50029800-50035600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:50030000-50035600	Weak transcription	HMEC	breast
16	chr12:50030800-50036400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:50030800-50038400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:50030800-50057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:50031000-50035600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:50031000-50036000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:50031000-50036200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:50031000-50036400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:50031200-50035400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:50031200-50035600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:50031200-50035600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:50031200-50036200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:50031200-50036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:50031200-50038200	Weak transcription	Stomach Mucosa	stomach
29	chr12:50031200-50038400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:50031200-50038600	Strong transcription	Fetal Intestine Large	intestine
31	chr12:50031200-50045600	Weak transcription	Small Intestine	intestine
32	chr12:50031400-50035000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:50031400-50035600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:50031400-50035600	Weak transcription	Right Ventricle	heart
35	chr12:50031400-50036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:50031400-50036000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:50031400-50036000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:50031400-50036000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:50031400-50036000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:50031400-50036200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:50031400-50036200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:50031400-50036200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:50031400-50036400	Weak transcription	Fetal Thymus	thymus
44	chr12:50031400-50036400	Weak transcription	Dnd41	blood
45	chr12:50031400-50038200	Weak transcription	Right Atrium	heart
46	chr12:50031400-50041800	Weak transcription	Fetal Brain Male	brain
47	chr12:50031600-50037800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:50031600-50052200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:50031800-50035200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:50031800-50035600	Weak transcription	H9 Cell Line	embryonic stem cell

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