Variant report

Variant	rs1057548
Chromosome Location	chr12:49522605-49522606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49520435-49522737	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:49521674-49522697	A549	lung:	n/a	n/a
3	POLR2A	chr12:49519438-49525993	GM12892	blood:	n/a	n/a
4	EP300	chr12:49522459-49522717	T-47D	breast:	n/a	n/a
5	POLR2A	chr12:49522517-49526329	SK-N-SH	brain:	n/a	n/a
6	HEY1	chr12:49520325-49525632	K562	blood:	n/a	chr12:49525016-49525031 chr12:49523999-49524014 chr12:49525182-49525197
7	POLR2A	chr12:49520242-49523256	U87	brain:	n/a	n/a
8	POLR2A	chr12:49522483-49525802	U87	brain:	n/a	n/a
9	POU2F2	chr12:49520600-49522729	GM12878	blood:	n/a	chr12:49521264-49521285
10	POLR2A	chr12:49520390-49525928	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:49522548-49523066	K562	blood:	n/a	n/a
12	POLR2A	chr12:49521563-49522742	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:49521611-49522731	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:49522599-49525738	PANC-1	pancreas:	n/a	n/a
15	HEY1	chr12:49520499-49522750	K562	blood:	n/a	n/a
16	POLR2A	chr12:49521653-49522649	A549	lung:	n/a	n/a
17	POLR2A	chr12:49520416-49525737	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:49519160-49525710	U87	brain:	n/a	n/a
19	POU2F2	chr12:49521627-49522746	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:49519189-49525680	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:49520104-49525589	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:49522546-49525640	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:49520159-49525725	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr12:49519868-49525630	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:49519435-49525804	GM12892	blood:	n/a	n/a
26	ZBTB33	chr12:49521522-49522768	K562	blood:	n/a	n/a
27	CTCF	chr12:49522482-49522688	T-47D	breast:	n/a	n/a
28	POLR2A	chr12:49520071-49525613	GM12891	blood:	n/a	n/a
29	POLR2A	chr12:49522476-49525646	K562	blood:	n/a	n/a
30	POLR2A	chr12:49519967-49525822	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr12:49521603-49522724	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:49520445-49522787	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:49519561-49525623	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr12:49521600-49522708	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:49519548-49525666	GM12892	blood:	n/a	n/a
36	POLR2A	chr12:49520195-49525833	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr12:49519414-49525811	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr12:49521666-49522743	A549	lung:	n/a	n/a
39	POLR2A	chr12:49520429-49522744	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:49520178-49525642	GM12891	blood:	n/a	n/a
41	POLR2A	chr12:49520433-49522721	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:49477289..49493962-chr12:49512467..49528127,64	K562	blood:
2	chr12:49478072..49490419-chr12:49518907..49527034,52	K562	blood:
3	chr12:49500412..49506796-chr12:49520694..49526646,13	MCF-7	breast:
4	chr12:49519485..49526890-chr12:49616239..49624332,15	K562	blood:
5	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:
6	chr12:49481723..49485881-chr12:49518387..49522804,4	MCF-7	breast:
7	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
8	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
9	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
10	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
11	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
12	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
13	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258017	TF binding region
ENSG00000167548	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000167550	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10747562	0.80[EUR][1000 genomes]
rs10783306	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783307	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783308	0.83[EUR][1000 genomes]
rs10875922	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10875924	0.83[EUR][1000 genomes]
rs10875925	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875927	0.81[EUR][1000 genomes]
rs10875928	0.81[EUR][1000 genomes]
rs10875930	0.83[EUR][1000 genomes]
rs11168862	0.80[EUR][1000 genomes]
rs11168867	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168874	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168884	0.83[EUR][1000 genomes]
rs11168885	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168888	0.83[EUR][1000 genomes]
rs11168890	0.83[EUR][1000 genomes]
rs11168894	0.83[EUR][1000 genomes]
rs11168895	0.83[EUR][1000 genomes]
rs11168902	0.81[EUR][1000 genomes]
rs11168903	0.80[EUR][1000 genomes]
rs11837207	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12227296	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12227610	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228775	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12229524	0.81[EUR][1000 genomes]
rs12229529	0.80[EUR][1000 genomes]
rs12306494	0.81[EUR][1000 genomes]
rs12318740	0.83[EUR][1000 genomes]
rs12579015	0.83[EUR][1000 genomes]
rs1476137	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476138	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1991427	0.83[EUR][1000 genomes]
rs2114845	0.83[EUR][1000 genomes]
rs2114846	0.84[EUR][1000 genomes]
rs2162644	0.82[EUR][1000 genomes]
rs2241727	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2753	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35884657	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57853986	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58336603	0.83[EUR][1000 genomes]
rs73110168	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311346	0.80[EUR][1000 genomes]
rs731350	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7954521	0.83[EUR][1000 genomes]
rs7957983	0.81[EUR][1000 genomes]
rs7958241	0.83[EUR][1000 genomes]
rs7958572	0.82[EUR][1000 genomes]
rs7969963	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7969967	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7976890	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7978448	0.83[EUR][1000 genomes]
rs7978659	0.84[EUR][1000 genomes]
rs9325145	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788139	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788140	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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	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	nsv975485	chr12:49521410-49525683	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	124 gene(s)	inside rSNPs	diseases
5	esv3417605	chr12:49521878-49578961	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 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	chr12:49515000-49522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:49515000-49522800	Weak transcription	Stomach Mucosa	stomach
3	chr12:49515200-49522800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:49519000-49522800	Weak transcription	Gastric	stomach
5	chr12:49519200-49523600	Weak transcription	Psoas Muscle	Psoas
6	chr12:49519400-49522800	Weak transcription	Brain Angular Gyrus	brain
7	chr12:49519600-49523600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:49520000-49523400	Weak transcription	Small Intestine	intestine
9	chr12:49520400-49522800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:49520400-49523000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:49520400-49523400	Strong transcription	Fetal Stomach	stomach
12	chr12:49520600-49522800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:49520600-49522800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:49520600-49522800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:49520600-49522800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:49520600-49522800	Strong transcription	Brain Hippocampus Middle	brain
17	chr12:49520600-49522800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:49520600-49522800	Strong transcription	HMEC	breast
19	chr12:49520600-49522800	Strong transcription	NH-A	brain
20	chr12:49520600-49523000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:49520600-49523000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:49520600-49523000	Strong transcription	Fetal Thymus	thymus
23	chr12:49520600-49523200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:49520600-49523200	Strong transcription	Fetal Intestine Large	intestine
25	chr12:49520600-49523200	Strong transcription	Placenta	Placenta
26	chr12:49520600-49523400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:49520600-49523400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:49520600-49523400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:49520800-49522800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:49520800-49522800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:49520800-49522800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:49520800-49522800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:49520800-49522800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:49520800-49522800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:49520800-49522800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr12:49520800-49522800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:49520800-49522800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr12:49520800-49522800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:49520800-49522800	Strong transcription	HUVEC	blood vessel
40	chr12:49520800-49522800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:49520800-49522800	Strong transcription	NHDF-Ad	bronchial
42	chr12:49520800-49523000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:49520800-49523000	Strong transcription	Brain Anterior Caudate	brain
44	chr12:49520800-49523000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr12:49520800-49523000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:49520800-49523000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:49520800-49523000	Strong transcription	Fetal Muscle Leg	muscle
48	chr12:49520800-49523000	Strong transcription	Left Ventricle	heart
49	chr12:49520800-49523000	Strong transcription	Pancreas	Pancrea
50	chr12:49520800-49523000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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