Variant report

Variant	rs28372890
Chromosome Location	chr12:12503519-12503520
allele	G/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	CTCF	chr12:12503380-12503530	GM12873	blood:	n/a	n/a
2	TBP	chr12:12502741-12503553	K562	blood:	n/a	n/a
3	MXI1	chr12:12502964-12503673	HepG2	liver:	n/a	n/a
4	CTCF	chr12:12503380-12503530	HRPEpiC	eye:	n/a	n/a
5	CTCF	chr12:12503266-12503563	GM12878	blood:	n/a	chr12:12503316-12503329
6	ZBTB7A	chr12:12502742-12503528	K562	blood:	n/a	n/a
7	POLR2A	chr12:12502592-12503584	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr12:12503380-12503530	WI-38	lung:	n/a	n/a
9	CTCF	chr12:12503400-12503550	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr12:12503246-12503524	K562	blood:	n/a	chr12:12503316-12503329
11	EP300	chr12:12502519-12503781	ECC-1	luminal epithelium:	n/a	chr12:12503344-12503360 chr12:12502973-12502989 chr12:12503398-12503411
12	POLR2A	chr12:12502706-12503559	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr12:12502587-12503521	PBDE	blood:	n/a	n/a
14	RAD21	chr12:12503238-12503548	HepG2	liver:	n/a	n/a
15	MAX	chr12:12503312-12503597	K562	blood:	n/a	n/a
16	CTCF	chr12:12503340-12503630	HCM	heart:	n/a	n/a
17	SIN3A	chr12:12502604-12503602	H1-hESC	embryonic stem cell:	n/a	chr12:12503380-12503391
18	E2F6	chr12:12502538-12503704	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA2	chr12:12503327-12504637	HepG2	liver:	n/a	n/a
20	CTCF	chr12:12503380-12503530	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr12:12503380-12503530	GM12878	blood:	n/a	n/a
22	CTCF	chr12:12503380-12503530	GM12864	blood:	n/a	n/a
23	CTCF	chr12:12503366-12503530	Kidney_OC	kidney:	n/a	n/a
24	CTCF	chr12:12503380-12503530	MCF-7	breast:	n/a	n/a
25	CTCF	chr12:12502422-12504119	A549	lung:	n/a	chr12:12503316-12503329
26	MYC	chr12:12502943-12503628	NB4	blood:	n/a	n/a
27	CTCF	chr12:12503380-12503530	HPF	lung:	n/a	n/a
28	MAX	chr12:12502653-12503614	SK-N-SH	brain:	n/a	n/a
29	RUNX3	chr12:12502909-12503569	GM12878	blood:	n/a	chr12:12503161-12503170 chr12:12503161-12503170 chr12:12503153-12503170
30	CTCF	chr12:12503400-12503550	GM12867	blood:	n/a	n/a
31	TCF12	chr12:12502709-12503698	ECC-1	luminal epithelium:	n/a	chr12:12502879-12502889
32	POLR2A	chr12:12502868-12503579	K562	blood:	n/a	n/a
33	MAX	chr12:12502581-12503686	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr12:12503380-12503530	HEK293	kidney:	n/a	n/a
35	CTCF	chr12:12503400-12503550	GM12872	blood:	n/a	n/a
36	TAF1	chr12:12502713-12503560	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr12:12503400-12503550	GM12865	blood:	n/a	n/a
38	MAX	chr12:12502596-12503737	ECC-1	luminal epithelium:	n/a	n/a
39	MYC	chr12:12503234-12503634	H1-hESC	embryonic stem cell:	n/a	n/a
40	SRF	chr12:12502527-12503652	ECC-1	luminal epithelium:	n/a	chr12:12502787-12502805 chr12:12502784-12502801 chr12:12503619-12503637 chr12:12502786-12502804 chr12:12502790-12502801 chr12:12502786-12502800 chr12:12502789-12502802 chr12:12502787-12502801
41	CTCF	chr12:12503349-12503531	A549	lung:	n/a	n/a
42	ZBTB7A	chr12:12503200-12503530	HepG2	liver:	n/a	n/a
43	CTCF	chr12:12503460-12503610	NB4	blood:	n/a	n/a
44	E2F6	chr12:12502758-12503642	A549	lung:	n/a	n/a
45	MAX	chr12:12502717-12503636	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr12:12502697-12503597	H1-hESC	embryonic stem cell:	n/a	chr12:12503316-12503329
47	ZBTB7A	chr12:12502615-12503817	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr12:12502782-12503592	A549	lung:	n/a	n/a
49	RAD21	chr12:12502620-12503570	H1-hESC	embryonic stem cell:	n/a	n/a
50	JUND	chr12:12503088-12503523	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12222045..12224389-chr12:12502260..12504688,2	K562	blood:
2	chr12:12502870..12504833-chr12:12508269..12511200,3	K562	blood:
3	chr12:12489787..12492519-chr12:12503031..12504558,2	MCF-7	breast:
4	chr12:12502650..12504579-chr12:12713839..12715957,2	MCF-7	breast:
5	chr12:12501597..12504303-chr12:12848029..12850251,2	K562	blood:
6	chr12:12501756..12503820-chr12:12509545..12511706,2	MCF-7	breast:
7	chr12:12502870..12505613-chr12:12507814..12511200,4	K562	blood:
8	chr12:12501083..12504981-chr12:12508403..12511914,10	MCF-7	breast:

Variant related genes	Relation type
MANSC1	TF binding region
ENSG00000111261	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000121380	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000243141	Chromatin interaction
ENSG00000183150	Chromatin interaction
ENSG00000205791	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17303178	0.85[EUR][1000 genomes]
rs17375328	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2160588	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3741798	0.90[EUR][1000 genomes]
rs3825259	0.90[EUR][1000 genomes]
rs55865572	0.89[EUR][1000 genomes]
rs55892345	0.90[EUR][1000 genomes]
rs56829405	0.90[EUR][1000 genomes]
rs57725255	0.96[EUR][1000 genomes]
rs61922023	0.85[EUR][1000 genomes]
rs61922024	0.85[EUR][1000 genomes]
rs61922025	0.85[EUR][1000 genomes]
rs61922026	0.85[EUR][1000 genomes]
rs61922027	0.85[EUR][1000 genomes]
rs61922028	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61922044	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61922045	0.91[EUR][1000 genomes]
rs61922046	0.88[EUR][1000 genomes]
rs61922047	0.89[EUR][1000 genomes]
rs61922049	0.89[EUR][1000 genomes]
rs61922054	0.96[EUR][1000 genomes]
rs61922057	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61922058	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73277486	0.88[EUR][1000 genomes]
rs73277491	0.88[EUR][1000 genomes]
rs73279305	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv898809	chr12:12488067-12509314	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12501400-12503800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:12501800-12504200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:12502000-12503600	Active TSS	Brain Anterior Caudate	brain
4	chr12:12502000-12503800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:12502000-12504200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:12502200-12503600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:12502200-12503600	Active TSS	Brain Hippocampus Middle	brain
8	chr12:12502200-12503600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr12:12502200-12503800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:12502200-12503800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:12502400-12503600	Active TSS	Brain Substantia Nigra	brain
12	chr12:12502400-12503600	Active TSS	Colon Smooth Muscle	Colon
13	chr12:12502400-12503600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr12:12502400-12503600	Active TSS	Esophagus	oesophagus
15	chr12:12502400-12503600	Active TSS	Pancreas	Pancrea
16	chr12:12502400-12503600	Active TSS	Right Atrium	heart
17	chr12:12502400-12503800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:12502400-12503800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:12502400-12503800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12502400-12503800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:12502400-12503800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr12:12502400-12503800	Active TSS	Aorta	Aorta
23	chr12:12502400-12503800	Active TSS	Fetal Kidney	kidney
24	chr12:12502400-12503800	Active TSS	Right Ventricle	heart
25	chr12:12502400-12504000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr12:12502400-12504000	Flanking Active TSS	NHEK	skin
27	chr12:12502400-12504200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr12:12502600-12503600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:12502600-12503600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:12502600-12503600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:12502600-12503600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:12502600-12503600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:12502600-12503600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr12:12502600-12503600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr12:12502600-12503600	Active TSS	Left Ventricle	heart
36	chr12:12502600-12503600	Active TSS	Lung	lung
37	chr12:12502600-12503600	Active TSS	Ovary	ovary
38	chr12:12502600-12503800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:12502600-12503800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:12502600-12503800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr12:12502600-12503800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:12502600-12503800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:12502600-12503800	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:12502600-12503800	Active TSS	Stomach Smooth Muscle	stomach
45	chr12:12502600-12503800	Active TSS	NHDF-Ad	bronchial
46	chr12:12502600-12503800	Active TSS	Osteobl	bone
47	chr12:12502600-12504000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr12:12502600-12504000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr12:12502600-12504200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:12502800-12503600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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