Variant report

Variant	rs59205218
Chromosome Location	chr12:48174275-48174276
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48173614-48174352	U87	brain:	n/a	n/a
2	POLR2A	chr12:48172670-48174400	SK-N-MC	brain:	n/a	n/a
3	STAT5A	chr12:48173611-48174383	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:48172706-48174303	A549	lung:	n/a	n/a
5	POLR2A	chr12:48173049-48174386	K562	blood:	n/a	n/a
6	POLR2A	chr12:48173029-48174300	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:48172869-48174326	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:48168539-48189348	K562	blood:	n/a	n/a
9	POLR2A	chr12:48172484-48174533	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr12:48172500-48174440	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr12:48173085-48174299	K562	blood:	n/a	n/a
12	POLR2A	chr12:48172711-48174370	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:48172863-48174311	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:48172975-48174454	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:48174140-48174290	HBMEC	blood vessel:	n/a	n/a
16	POLR2A	chr12:48173754-48174291	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:48172625-48174350	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr12:48172733-48176227	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr12:48172713-48174301	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr12:48172812-48174313	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:48172598-48174336	A549	lung:	n/a	n/a
22	POLR2A	chr12:48172652-48174350	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:48174169-48174288	ProgFib	skin:	n/a	n/a
24	POLR2A	chr12:48172518-48174340	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr12:48172596-48174362	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr12:48173742-48174315	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:48173739-48174281	A549	lung:	n/a	n/a
28	POLR2A	chr12:48172715-48174317	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:48173549..48176410-chr12:48184370..48186817,3	K562	blood:
2	chr12:48164603..48170216-chr12:48170812..48178110,12	MCF-7	breast:
3	chr12:48173973..48175835-chr12:48212326..48213982,2	K562	blood:
4	chr12:48135977..48137705-chr12:48172310..48175279,2	K562	blood:
5	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
6	chr12:48135925..48137862-chr12:48173853..48176277,2	MCF-7	breast:
7	chr12:48173992..48175896-chr12:48221117..48223369,2	MCF-7	breast:
8	chr12:48100044..48102327-chr12:48172269..48174749,2	K562	blood:
9	chr12:48174206..48174811-chr12:48231769..48232567,2	K562	blood:
10	chr12:48099987..48101621-chr12:48172396..48174899,2	MCF-7	breast:
11	chr12:48173236..48178017-chr12:48212091..48216621,8	MCF-7	breast:
12	chr12:48111607..48113554-chr12:48173778..48176264,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268069	TF binding region
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000257488	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1006476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1006477	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58067800	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60776348	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7135791	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7306788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7307367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73291230	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7488942	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7964310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168000-48174800	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48168000-48175000	Weak transcription	NH-A	brain
3	chr12:48168000-48175400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48168000-48177200	Weak transcription	Small Intestine	intestine
5	chr12:48168200-48174800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48168200-48175600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:48168400-48174800	Weak transcription	Primary T cells from cord blood	blood
9	chr12:48168600-48175600	Weak transcription	Liver	Liver
10	chr12:48168600-48178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:48169000-48177600	Weak transcription	Dnd41	blood
12	chr12:48169200-48177600	Weak transcription	Fetal Lung	lung
13	chr12:48169200-48178600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:48169400-48179200	Weak transcription	Fetal Kidney	kidney
15	chr12:48169800-48181200	Weak transcription	GM12878-XiMat	blood
16	chr12:48170400-48174600	Weak transcription	Thymus	Thymus
17	chr12:48170400-48174800	Weak transcription	Pancreas	Pancrea
18	chr12:48170600-48181200	Weak transcription	HepG2	liver
19	chr12:48171400-48175000	Weak transcription	NHLF	lung
20	chr12:48172000-48174600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:48172200-48175800	Weak transcription	Primary B cells from cord blood	blood
22	chr12:48172200-48177600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:48172400-48174800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:48172400-48174800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:48172400-48175000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:48172400-48175000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:48172400-48175200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:48172400-48175600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:48172400-48175600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:48172400-48175800	Weak transcription	HSMM	muscle
31	chr12:48172400-48176000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:48172400-48176200	Weak transcription	HUVEC	blood vessel
33	chr12:48172400-48177400	Weak transcription	HSMMtube	muscle
34	chr12:48172800-48175600	Weak transcription	Hela-S3	cervix
35	chr12:48173000-48174600	Weak transcription	Lung	lung
36	chr12:48173000-48174800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:48173000-48175000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:48173000-48175000	Weak transcription	Colonic Mucosa	Colon
39	chr12:48173000-48175200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:48173000-48175600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:48173000-48175600	Weak transcription	NHDF-Ad	bronchial
42	chr12:48173000-48177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:48173000-48177000	Weak transcription	Psoas Muscle	Psoas
44	chr12:48173000-48192400	Weak transcription	Right Atrium	heart
45	chr12:48173200-48174600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:48173200-48174800	Weak transcription	Ovary	ovary
47	chr12:48173200-48175000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:48173200-48175000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:48173200-48175000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:48173200-48175000	Weak transcription	HMEC	breast

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