Variant report

Variant	rs824737
Chromosome Location	chr12:42539813-42539814
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	TCF12	chr12:42538262-42539894	A549	lung:	n/a	chr12:42539655-42539663
2	WRNIP1	chr12:42538635-42540104	GM12878	blood:	n/a	n/a
3	RAD21	chr12:42539476-42539838	A549	lung:	n/a	n/a
4	KAP1	chr12:42538386-42539924	HEK293	kidney:	n/a	n/a
5	MAZ	chr12:42537925-42539956	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
6	MYC	chr12:42537683-42539853	NB4	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
7	RAD21	chr12:42539347-42539930	A549	lung:	n/a	n/a
8	MAX	chr12:42537142-42540046	NB4	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
9	RAD21	chr12:42539330-42539886	HCT-116	colon:	n/a	n/a
10	MAX	chr12:42537100-42539866	A549	lung:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
11	NR3C1	chr12:42539351-42539814	A549	lung:	n/a	chr12:42539568-42539582 chr12:42539568-42539582 chr12:42539565-42539586 chr12:42539567-42539584
12	CTCF	chr12:42539195-42539852	K562	blood:	n/a	n/a
13	CUX1	chr12:42539168-42539977	K562	blood:	n/a	n/a
14	ARID3A	chr12:42539495-42539897	K562	blood:	n/a	n/a
15	KAP1	chr12:42539257-42539850	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:42536858..42540358-chr12:42630016..42633914,10	MCF-7	breast:
2	chr12:42537005..42540223-chr12:42630265..42633071,6	MCF-7	breast:
3	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
4	chr12:42537957..42540928-chr12:42622624..42625244,2	MCF-7	breast:
5	chr12:42537704..42540061-chr12:42725418..42727107,2	K562	blood:
6	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
7	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
8	chr12:42536402..42539877-chr12:42717128..42721445,5	MCF-7	breast:
9	chr12:42539265..42541316-chr12:42719076..42720974,2	K562	blood:
10	chr12:42537508..42540547-chr12:42555328..42558210,3	MCF-7	breast:
11	chr12:42537037..42538708-chr12:42539498..42541972,3	MCF-7	breast:

Variant related genes	Relation type
GXYLT1	TF binding region
ENSG00000151233	Chromatin interaction
ENSG00000269367	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1009721	1.00[EUR][1000 genomes]
rs11118	1.00[EUR][1000 genomes]
rs11829542	1.00[EUR][1000 genomes]
rs11830248	1.00[EUR][1000 genomes]
rs11833381	1.00[EUR][1000 genomes]
rs1233989	1.00[EUR][1000 genomes]
rs1233991	1.00[EUR][1000 genomes]
rs1233993	1.00[EUR][1000 genomes]
rs1234007	1.00[EUR][1000 genomes]
rs1234031	1.00[EUR][1000 genomes]
rs1234041	1.00[EUR][1000 genomes]
rs1234103	1.00[EUR][1000 genomes]
rs1238283	1.00[EUR][1000 genomes]
rs1626596	1.00[EUR][1000 genomes]
rs1628339	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1683199	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1683203	1.00[EUR][1000 genomes]
rs1688846	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1688876	1.00[EUR][1000 genomes]
rs17091023	1.00[EUR][1000 genomes]
rs1873684	1.00[EUR][1000 genomes]
rs2639131	1.00[EUR][1000 genomes]
rs57435495	1.00[EUR][1000 genomes]
rs58229270	1.00[EUR][1000 genomes]
rs58676357	1.00[EUR][1000 genomes]
rs60314019	1.00[EUR][1000 genomes]
rs7305651	1.00[EUR][1000 genomes]
rs73270269	1.00[EUR][1000 genomes]
rs73278244	1.00[EUR][1000 genomes]
rs73278291	1.00[EUR][1000 genomes]
rs73280009	1.00[EUR][1000 genomes]
rs73280011	1.00[EUR][1000 genomes]
rs73281814	1.00[EUR][1000 genomes]
rs73281820	1.00[EUR][1000 genomes]
rs73281838	1.00[EUR][1000 genomes]
rs73281851	1.00[EUR][1000 genomes]
rs73281860	1.00[EUR][1000 genomes]
rs73281880	1.00[EUR][1000 genomes]
rs73281886	1.00[EUR][1000 genomes]
rs73281894	1.00[EUR][1000 genomes]
rs73283707	1.00[EUR][1000 genomes]
rs73283734	1.00[EUR][1000 genomes]
rs73283759	1.00[EUR][1000 genomes]
rs73283792	1.00[EUR][1000 genomes]
rs73283799	1.00[EUR][1000 genomes]
rs73285617	1.00[EUR][1000 genomes]
rs73285619	1.00[EUR][1000 genomes]
rs73285621	1.00[EUR][1000 genomes]
rs73285641	1.00[EUR][1000 genomes]
rs73285662	1.00[EUR][1000 genomes]
rs73285670	1.00[EUR][1000 genomes]
rs7970895	1.00[EUR][1000 genomes]
rs824690	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824696	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824698	1.00[EUR][1000 genomes]
rs824715	1.00[EUR][1000 genomes]
rs824719	1.00[EUR][1000 genomes]
rs824720	1.00[EUR][1000 genomes]
rs824721	1.00[EUR][1000 genomes]
rs824723	1.00[EUR][1000 genomes]
rs824725	1.00[EUR][1000 genomes]
rs824727	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824729	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824731	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824732	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824733	1.00[EUR][1000 genomes]
rs824735	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs844045	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs850964	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs850965	0.91[AFR][1000 genomes];1.00[EUR][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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42537400-42540000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:42539000-42540000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr12:42539200-42540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:42539200-42552200	Weak transcription	HSMM	muscle
5	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:42539400-42540000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:42539400-42540000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr12:42539400-42540000	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:42539400-42540000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:42539400-42540000	Enhancers	Stomach Mucosa	stomach
11	chr12:42539400-42540400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:42539400-42541000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:42539400-42551400	Weak transcription	Primary B cells from cord blood	blood
14	chr12:42539400-42551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
19	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:42539600-42540000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:42539600-42540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:42539600-42540000	Enhancers	Fetal Intestine Large	intestine
23	chr12:42539600-42540000	Enhancers	Fetal Intestine Small	intestine
24	chr12:42539600-42540000	Enhancers	HepG2	liver
25	chr12:42539600-42540200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr12:42539600-42540200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr12:42539600-42540200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:42539600-42540400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:42539600-42540600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:42539600-42550200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:42539600-42550800	Weak transcription	Primary T cells from cord blood	blood
32	chr12:42539600-42550800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:42539600-42551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:42539600-42551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:42539600-42552200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:42539600-42552400	Weak transcription	HUVEC	blood vessel
37	chr12:42539600-42553600	Weak transcription	Adipose Nuclei	Adipose
38	chr12:42539600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:42539600-42553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
41	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
42	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
44	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:42539800-42540000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:42539800-42540000	Enhancers	Brain Anterior Caudate	brain
47	chr12:42539800-42540200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr12:42539800-42540400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr12:42539800-42540400	Enhancers	K562	blood
50	chr12:42539800-42541000	Enhancers	A549	lung

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