Variant report

Variant	rs10880255
Chromosome Location	chr12:42539761-42539762
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	RCOR1	chr12:42538467-42539795	K562	blood:	n/a	n/a
2	NR3C1	chr12:42539369-42539805	A549	lung:	n/a	chr12:42539568-42539582 chr12:42539568-42539582 chr12:42539565-42539586 chr12:42539567-42539584
3	JUND	chr12:42538117-42539779	K562	blood:	n/a	n/a
4	TCF12	chr12:42538262-42539894	A549	lung:	n/a	chr12:42539655-42539663
5	WRNIP1	chr12:42538635-42540104	GM12878	blood:	n/a	n/a
6	RAD21	chr12:42539321-42539809	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr12:42539476-42539838	A549	lung:	n/a	n/a
8	KAP1	chr12:42538386-42539924	HEK293	kidney:	n/a	n/a
9	CTCF	chr12:42539640-42539790	A549	lung:	n/a	n/a
10	MAZ	chr12:42537925-42539956	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
11	CTCF	chr12:42539640-42539790	K562	blood:	n/a	n/a
12	CTCF	chr12:42539620-42539770	GM12866	blood:	n/a	n/a
13	FOXA1	chr12:42539226-42539762	A549	lung:	n/a	n/a
14	MYC	chr12:42537683-42539853	NB4	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
15	RCOR1	chr12:42537847-42539782	K562	blood:	n/a	n/a
16	CTCF	chr12:42539620-42539770	GM12864	blood:	n/a	n/a
17	RAD21	chr12:42539376-42539773	H1-hESC	embryonic stem cell:	n/a	n/a
18	BHLHE40	chr12:42538218-42539801	K562	blood:	n/a	chr12:42538556-42538572 chr12:42538554-42538570 chr12:42538553-42538569
19	RAD21	chr12:42539347-42539930	A549	lung:	n/a	n/a
20	POLR2A	chr12:42538074-42539801	K562	blood:	n/a	n/a
21	MAX	chr12:42537142-42540046	NB4	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
22	CTCF	chr12:42539640-42539790	GM06990	blood:	n/a	n/a
23	CTCF	chr12:42539640-42539790	AG04450	lung:	n/a	n/a
24	RAD21	chr12:42539464-42539772	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr12:42539330-42539886	HCT-116	colon:	n/a	n/a
26	MYC	chr12:42537506-42539801	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
27	CTCF	chr12:42539620-42539770	SAEC	small airway:	n/a	n/a
28	RAD21	chr12:42539484-42539802	SK-N-SH_RA	brain:	n/a	n/a
29	MAX	chr12:42537100-42539866	A549	lung:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
30	CTCF	chr12:42539620-42539770	HAc	cerebellar:	n/a	n/a
31	NR3C1	chr12:42539351-42539814	A549	lung:	n/a	chr12:42539568-42539582 chr12:42539568-42539582 chr12:42539565-42539586 chr12:42539567-42539584
32	CTCF	chr12:42539620-42539770	HRE	kidney:	n/a	n/a
33	CTCF	chr12:42539195-42539852	K562	blood:	n/a	n/a
34	CTCF	chr12:42539385-42539811	A549	lung:	n/a	n/a
35	CUX1	chr12:42539168-42539977	K562	blood:	n/a	n/a
36	ARID3A	chr12:42539495-42539897	K562	blood:	n/a	n/a
37	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
ENSG00000015153	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000269367	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11181340	0.93[ASN][1000 genomes]
rs11181341	0.93[ASN][1000 genomes]
rs11181345	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11181363	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.88[YRI][hapmap]
rs7135955	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap]

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:73 , 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	chr12:42538800-42539800	Flanking Active TSS	K562	blood
3	chr12:42539000-42539800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:42539000-42539800	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr12:42539000-42540000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr12:42539200-42539800	Enhancers	Esophagus	oesophagus
7	chr12:42539200-42539800	Enhancers	Fetal Muscle Leg	muscle
8	chr12:42539200-42539800	Enhancers	Spleen	Spleen
9	chr12:42539200-42539800	Flanking Active TSS	A549	lung
10	chr12:42539200-42540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:42539200-42552200	Weak transcription	HSMM	muscle
12	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:42539400-42539800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:42539400-42539800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:42539400-42539800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:42539400-42539800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:42539400-42539800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:42539400-42539800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:42539400-42539800	Enhancers	Fetal Heart	heart
20	chr12:42539400-42539800	Enhancers	Fetal Kidney	kidney
21	chr12:42539400-42539800	Enhancers	Fetal Lung	lung
22	chr12:42539400-42539800	Enhancers	Placenta	Placenta
23	chr12:42539400-42539800	Enhancers	Hela-S3	cervix
24	chr12:42539400-42540000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:42539400-42540000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr12:42539400-42540000	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:42539400-42540000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:42539400-42540000	Enhancers	Stomach Mucosa	stomach
29	chr12:42539400-42540400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:42539400-42541000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:42539400-42551400	Weak transcription	Primary B cells from cord blood	blood
32	chr12:42539400-42551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
37	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:42539600-42539800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
39	chr12:42539600-42539800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
40	chr12:42539600-42539800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:42539600-42539800	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:42539600-42539800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:42539600-42539800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:42539600-42539800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr12:42539600-42539800	Enhancers	Pancreas	Pancrea
46	chr12:42539600-42539800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:42539600-42539800	Bivalent Enhancer	Dnd41	blood
48	chr12:42539600-42539800	Enhancers	GM12878-XiMat	blood
49	chr12:42539600-42540000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:42539600-42540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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