Variant report

Variant	rs12322282
Chromosome Location	chr12:42539143-42539144
allele	C/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	BACH1	chr12:42538606-42539221	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:42538038-42539285	Hela-S3	cervix:	n/a	chr12:42538561-42538571 chr12:42538746-42538755 chr12:42538558-42538568 chr12:42538555-42538565
3	POLR2A	chr12:42538244-42539252	U87	brain:	n/a	n/a
4	POLR2A	chr12:42538047-42539301	GM19099	blood:	n/a	n/a
5	POLR2A	chr12:42538251-42539718	PBDE	blood:	n/a	n/a
6	TBL1XR1	chr12:42538373-42539556	K562	blood:	n/a	n/a
7	POLR2A	chr12:42537957-42539336	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr12:42538541-42539296	HepG2	liver:	n/a	n/a
9	GTF2F1	chr12:42538526-42539390	K562	blood:	n/a	n/a
10	MAX	chr12:42538250-42539452	GM12878	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
11	POLR2A	chr12:42537266-42539525	Hela-S3	cervix:	n/a	n/a
12	BCL3	chr12:42538495-42539699	A549	lung:	n/a	chr12:42538554-42538567 chr12:42538556-42538569 chr12:42538553-42538566 chr12:42538503-42538512 chr12:42538559-42538572 chr12:42538562-42538571 chr12:42538563-42538576 chr12:42538523-42538536 chr12:42538559-42538568
13	POLR2A	chr12:42538097-42539200	HUVEC	blood vessel:	n/a	n/a
14	ARID3A	chr12:42538586-42539219	K562	blood:	n/a	n/a
15	EP300	chr12:42538124-42539297	ECC-1	luminal epithelium:	n/a	chr12:42538519-42538535 chr12:42538719-42538735 chr12:42538558-42538567 chr12:42538561-42538570
16	POLR2A	chr12:42538439-42539671	K562	blood:	n/a	n/a
17	TBP	chr12:42538579-42539323	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr12:42538501-42539199	MCF-7	breast:	n/a	n/a
19	POLR2A	chr12:42538299-42539209	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:42537845-42539754	Raji	blood:	n/a	n/a
21	TBP	chr12:42538275-42539244	H1-hESC	embryonic stem cell:	n/a	n/a
22	BHLHE40	chr12:42538416-42539375	GM12878	blood:	n/a	chr12:42538556-42538572 chr12:42538554-42538570 chr12:42538553-42538569
23	TFAP2C	chr12:42537838-42539271	Hela-S3	cervix:	n/a	chr12:42538818-42538833
24	PML	chr12:42538276-42539218	GM12878	blood:	n/a	n/a
25	CBX3	chr12:42538497-42539742	K562	blood:	n/a	n/a
26	POLR2A	chr12:42538121-42539180	GM18526	blood:	n/a	n/a
27	MTA3	chr12:42538490-42539603	GM12878	blood:	n/a	n/a
28	MAX	chr12:42537795-42539367	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
29	RCOR1	chr12:42538467-42539795	K562	blood:	n/a	n/a
30	POLR2A	chr12:42538303-42539347	K562	blood:	n/a	n/a
31	TEAD4	chr12:42538400-42539740	K562	blood:	n/a	n/a
32	CREB1	chr12:42538269-42539255	HepG2	liver:	n/a	n/a
33	E2F6	chr12:42538511-42539393	H1-hESC	embryonic stem cell:	n/a	chr12:42538561-42538571 chr12:42538746-42538755 chr12:42538558-42538568 chr12:42538555-42538565
34	MAX	chr12:42538134-42539251	HCT-116	colon:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
35	MAX	chr12:42538448-42539270	A549	lung:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
36	POLR2A	chr12:42538046-42539317	MCF10A-Er-Src	breast:	n/a	n/a
37	MXI1	chr12:42536964-42539693	SK-N-SH	brain:	n/a	n/a
38	SIN3A	chr12:42537366-42539215	H1-hESC	embryonic stem cell:	n/a	chr12:42538521-42538532
39	MYC	chr12:42539134-42539179	K562	blood:	n/a	n/a
40	CEBPB	chr12:42538552-42539246	K562	blood:	n/a	n/a
41	EP300	chr12:42538112-42539170	SK-N-SH	brain:	n/a	chr12:42538519-42538535 chr12:42538719-42538735 chr12:42538558-42538567 chr12:42538561-42538570
42	JUND	chr12:42538117-42539779	K562	blood:	n/a	n/a
43	PML	chr12:42538344-42539260	K562	blood:	n/a	n/a
44	POLR2A	chr12:42538078-42539725	NB4	blood:	n/a	n/a
45	CEBPB	chr12:42538401-42539186	A549	lung:	n/a	n/a
46	HEY1	chr12:42538192-42539275	K562	blood:	n/a	n/a
47	TCF12	chr12:42538262-42539894	A549	lung:	n/a	chr12:42539655-42539663
48	RUNX3	chr12:42538127-42539190	GM12878	blood:	n/a	n/a
49	WRNIP1	chr12:42538635-42540104	GM12878	blood:	n/a	n/a
50	TCF7L2	chr12:42538345-42539376	Hela-S3	cervix:	n/a	chr12:42539268-42539282

No.	Distal block	Cell Line	Cell type
1	chr12:42538608..42539586-chr6:26056616..26057177,2	NB4	blood:
2	chr12:42536858..42540358-chr12:42630016..42633914,10	MCF-7	breast:
3	chr12:42537136..42539433-chr12:42719521..42721782,2	K562	blood:
4	chr12:42537005..42540223-chr12:42630265..42633071,6	MCF-7	breast:
5	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
6	chr12:42537957..42540928-chr12:42622624..42625244,2	MCF-7	breast:
7	chr12:42537704..42540061-chr12:42725418..42727107,2	K562	blood:
8	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
9	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
10	chr12:42536402..42539877-chr12:42717128..42721445,5	MCF-7	breast:
11	chr12:42538708..42539351-chr17:73286140..73286679,2	NB4	blood:
12	chr12:42537508..42540547-chr12:42555328..42558210,3	MCF-7	breast:
13	chr12:42538702..42539493-chr17:54990934..54991901,2	NB4	blood:

Variant related genes	Relation type
GXYLT1	TF binding region
ENSG00000269367	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000121060	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000187837	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11181316	1.00[AMR][1000 genomes]
rs11181323	1.00[AMR][1000 genomes]
rs11181352	1.00[AMR][1000 genomes]
rs11181358	1.00[AMR][1000 genomes]
rs11181365	1.00[AMR][1000 genomes]
rs12298117	1.00[AMR][1000 genomes]
rs12299325	1.00[AMR][1000 genomes]
rs12300748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300940	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306988	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310121	1.00[AMR][1000 genomes]
rs12310800	1.00[AMR][1000 genomes]
rs12311173	1.00[AMR][1000 genomes]
rs12312552	1.00[AMR][1000 genomes]
rs12313439	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313898	1.00[AMR][1000 genomes]
rs12319636	1.00[AMR][1000 genomes]
rs12322316	1.00[AMR][1000 genomes]
rs12322344	1.00[AMR][1000 genomes]
rs12322394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12385814	1.00[AMR][1000 genomes]
rs28431054	1.00[AMR][1000 genomes]
rs28599887	1.00[AMR][1000 genomes]
rs56736670	1.00[AMR][1000 genomes]
rs58977672	1.00[AMR][1000 genomes]
rs61023006	1.00[AMR][1000 genomes]
rs6582387	1.00[AMR][1000 genomes]
rs6582388	1.00[AMR][1000 genomes]
rs7306048	1.00[AMR][1000 genomes]
rs7959000	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7971397	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974036	1.00[AMR][1000 genomes]
rs7976241	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3327626	chr12:42537735-42540233	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 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	chr12:42536800-42539400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:42537000-42539200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:42537000-42539200	Active TSS	Lung	lung
4	chr12:42537000-42539400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:42537000-42539600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:42537200-42539200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:42537200-42539200	Active TSS	A549	lung
8	chr12:42537200-42539200	Active TSS	HSMMtube	muscle
9	chr12:42537200-42539400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr12:42537200-42539400	Active TSS	Left Ventricle	heart
11	chr12:42537200-42539400	Active TSS	Right Atrium	heart
12	chr12:42537400-42539200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:42537400-42539200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:42537400-42539200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:42537400-42539200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:42537400-42539200	Active TSS	Aorta	Aorta
17	chr12:42537400-42539200	Active TSS	Esophagus	oesophagus
18	chr12:42537400-42539200	Active TSS	Ovary	ovary
19	chr12:42537400-42539200	Active TSS	Pancreas	Pancrea
20	chr12:42537400-42539400	Active TSS	Fetal Muscle Trunk	muscle
21	chr12:42537400-42539600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:42537400-42539600	Active TSS	Colonic Mucosa	Colon
23	chr12:42537400-42540000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr12:42537600-42539200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:42537600-42539200	Active TSS	Fetal Intestine Large	intestine
26	chr12:42537600-42539200	Active TSS	Psoas Muscle	Psoas
27	chr12:42537600-42539400	Active TSS	Brain Germinal Matrix	brain
28	chr12:42537600-42539400	Active TSS	Fetal Brain Female	brain
29	chr12:42537600-42539400	Active TSS	Right Ventricle	heart
30	chr12:42537800-42539200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:42537800-42539200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:42537800-42539200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:42537800-42539200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:42537800-42539200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr12:42537800-42539200	Active TSS	Colon Smooth Muscle	Colon
36	chr12:42537800-42539200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr12:42537800-42539400	Active TSS	Gastric	stomach
38	chr12:42537800-42539600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:42537800-42539600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:42537800-42539600	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr12:42538000-42539200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:42538000-42539200	Active TSS	Spleen	Spleen
43	chr12:42538000-42539400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr12:42538000-42539600	Active TSS	Stomach Smooth Muscle	stomach
45	chr12:42538400-42539400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:42538400-42539400	Active TSS	Thymus	Thymus
47	chr12:42538600-42539400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:42538600-42539600	Flanking Bivalent TSS/Enh	Dnd41	blood
49	chr12:42538800-42539200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:42538800-42539200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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