Variant report

Variant	rs28364704
Chromosome Location	chr12:50677434-50677435
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:393)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:393 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:50677077-50677720	H1-hESC	embryonic stem cell:	n/a	chr12:50677535-50677544
2	POLR2A	chr12:50677103-50678055	PANC-1	pancreas:	n/a	n/a
3	SRF	chr12:50676530-50677745	ECC-1	luminal epithelium:	n/a	n/a
4	YY1	chr12:50677208-50677645	GM12892	blood:	n/a	n/a
5	HCFC1	chr12:50677024-50677785	K562	blood:	n/a	n/a
6	POLR2A	chr12:50677168-50677738	GM12891	blood:	n/a	n/a
7	SIN3AK20	chr12:50677341-50677538	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:50677070-50678421	HepG2	liver:	n/a	n/a
9	POU2F2	chr12:50677290-50677642	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:50677021-50677850	U87	brain:	n/a	n/a
11	CTCF	chr12:50677380-50677530	GM12873	blood:	n/a	n/a
12	POU2F2	chr12:50677218-50677725	GM12878	blood:	n/a	n/a
13	NRF1	chr12:50677209-50677488	H1-hESC	embryonic stem cell:	n/a	chr12:50677383-50677394
14	POLR2A	chr12:50676957-50677967	SK-N-MC	brain:	n/a	n/a
15	MAX	chr12:50677107-50677726	K562	blood:	n/a	chr12:50677535-50677544
16	CTCF	chr12:50677380-50677530	BJ	skin:	n/a	n/a
17	CTCF	chr12:50677400-50677550	GM12873	blood:	n/a	n/a
18	MYC	chr12:50677204-50677836	MCF10A-Er-Src	breast:	n/a	chr12:50677535-50677544
19	ZNF143	chr12:50677226-50678226	K562	blood:	n/a	chr12:50677446-50677456
20	POLR2A	chr12:50677093-50677849	GM19193	blood:	n/a	n/a
21	MAX	chr12:50676825-50677962	ECC-1	luminal epithelium:	n/a	chr12:50677535-50677544
22	REST	chr12:50677327-50677657	HepG2	liver:	n/a	chr12:50677440-50677453 chr12:50677445-50677455
23	CTCF	chr12:50677374-50677508	GM12878	blood:	n/a	n/a
24	CTCF	chr12:50677400-50677550	BJ	skin:	n/a	n/a
25	POLR2A	chr12:50676998-50678423	K562	blood:	n/a	n/a
26	FOXM1	chr12:50677145-50677809	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:50677044-50678417	K562	blood:	n/a	n/a
28	POLR2A	chr12:50677087-50677957	GM12891	blood:	n/a	n/a
29	E2F4	chr12:50676901-50677502	MCF10A-Er-Src	breast:	n/a	n/a
30	CTCF	chr12:50677380-50677530	HCPEpiC	choroid plexus:	n/a	n/a
31	ELK1	chr12:50677395-50677572	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:50677052-50677684	HCT-116	colon:	n/a	n/a
33	MAX	chr12:50677000-50677715	H1-hESC	embryonic stem cell:	n/a	chr12:50677535-50677544
34	TAF1	chr12:50677085-50677598	HepG2	liver:	n/a	n/a
35	CTCF	chr12:50677360-50677510	HUVEC	blood vessel:	n/a	n/a
36	HEY1	chr12:50677081-50678418	K562	blood:	n/a	n/a
37	POLR2A	chr12:50677194-50677693	HL-60	blood:	n/a	n/a
38	TAF1	chr12:50677342-50677600	GM12891	blood:	n/a	n/a
39	CTCF	chr12:50677340-50677490	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr12:50677340-50677490	HCT-116	colon:	n/a	n/a
41	TAF1	chr12:50677341-50677529	GM12892	blood:	n/a	n/a
42	ZBTB7A	chr12:50677207-50677492	K562	blood:	n/a	n/a
43	TAF1	chr12:50676774-50678002	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr12:50677101-50677883	GM12892	blood:	n/a	n/a
45	POLR2A	chr12:50677107-50677707	A549	lung:	n/a	n/a
46	RAD21	chr12:50677356-50677474	K562	blood:	n/a	n/a
47	POLR2A	chr12:50677047-50677732	SK-N-SH	brain:	n/a	n/a
48	REST	chr12:50677260-50677607	SK-N-SH	brain:	n/a	chr12:50677440-50677453 chr12:50677445-50677455
49	TAF1	chr12:50677111-50677663	H1-neurons	neurons:	n/a	n/a
50	CTCF	chr12:50677380-50677530	AG04449	skin:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50677350..50679861-chr12:50792501..50795030,2	K562	blood:
2	chr1:150521379..150521971-chr12:50677163..50677877,2	NB4	blood:
3	chr12:50641106..50644296-chr12:50675797..50678807,3	K562	blood:
4	chr12:50676951..50677680-chr3:43731810..43732785,2	NB4	blood:
5	chr12:50467357..50469479-chr12:50676933..50678853,2	K562	blood:
6	chr12:50675775..50678031-chr6:7107823..7110608,2	MCF-7	breast:
7	chr12:50676754..50678948-chr12:132378610..132380632,2	MCF-7	breast:
8	chr12:50593299..50595374-chr12:50677220..50679734,2	K562	blood:
9	chr12:50676871..50679447-chr12:50689934..50691681,2	K562	blood:
10	chr12:50677251..50678858-chr12:50683227..50685287,2	MCF-7	breast:
11	chr12:50614322..50618314-chr12:50675052..50679891,5	K562	blood:
12	chr12:50617895..50619664-chr12:50676207..50678789,2	MCF-7	breast:
13	chr12:50677315..50677913-chr13:111267621..111268237,2	Hela-S3	cervix:
14	chr12:50504614..50508392-chr12:50676689..50680044,5	K562	blood:

No data

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000161813	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000124782	Chromatin interaction
ENSG00000203432	Chromatin interaction
ENSG00000203431	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000160746	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000269529	Chromatin interaction
ENSG00000177169	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000143382	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10747572	0.93[ASN][1000 genomes]
rs10783346	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783347	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12423130	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3815671	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7302422	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs736167	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974834	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8181651	0.95[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50674400-50677800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:50674600-50677600	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:50674600-50677800	Active TSS	Fetal Intestine Large	intestine
4	chr12:50674800-50678000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:50675000-50677600	Active TSS	Colonic Mucosa	Colon
6	chr12:50675200-50677600	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:50675200-50677600	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:50675400-50677800	Active TSS	Small Intestine	intestine
9	chr12:50675600-50677600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:50675800-50677600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:50675800-50677600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:50675800-50677600	Active TSS	Fetal Stomach	stomach
13	chr12:50675800-50677600	Active TSS	NHLF	lung
14	chr12:50675800-50678000	Active TSS	Aorta	Aorta
15	chr12:50676000-50677800	Active TSS	HSMMtube	muscle
16	chr12:50676000-50678400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:50676200-50677600	Active TSS	Fetal Brain Female	brain
18	chr12:50676200-50677800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:50676200-50678400	Active TSS	Pancreas	Pancrea
20	chr12:50676400-50677600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr12:50676400-50677600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:50676400-50677600	Active TSS	NHDF-Ad	bronchial
23	chr12:50676400-50677800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:50676400-50677800	Active TSS	Brain Angular Gyrus	brain
25	chr12:50676400-50677800	Active TSS	Colon Smooth Muscle	Colon
26	chr12:50676400-50677800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr12:50676400-50677800	Active TSS	Stomach Mucosa	stomach
28	chr12:50676400-50678000	Active TSS	Brain Substantia Nigra	brain
29	chr12:50676400-50678000	Active TSS	Esophagus	oesophagus
30	chr12:50676400-50678000	Active TSS	Gastric	stomach
31	chr12:50676400-50678200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:50676400-50678200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:50676400-50678200	Active TSS	Fetal Kidney	kidney
34	chr12:50676400-50678200	Active TSS	Right Ventricle	heart
35	chr12:50676400-50678600	Flanking Active TSS	Liver	Liver
36	chr12:50676600-50677600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:50676600-50677600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:50676600-50677600	Active TSS	Fetal Intestine Small	intestine
39	chr12:50676600-50677600	Active TSS	Osteobl	bone
40	chr12:50676600-50677800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:50676600-50677800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:50676600-50677800	Active TSS	Fetal Heart	heart
43	chr12:50676600-50677800	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:50676600-50677800	Active TSS	Left Ventricle	heart
45	chr12:50676600-50677800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr12:50676600-50677800	Active TSS	GM12878-XiMat	blood
47	chr12:50676600-50677800	Active TSS	HSMM	muscle
48	chr12:50676600-50678000	Active TSS	Lung	lung
49	chr12:50676600-50678200	Active TSS	Psoas Muscle	Psoas
50	chr12:50676600-50678400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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