Variant report

Variant	rs11181345
Chromosome Location	chr12:42539598-42539599
allele	C/G
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	chr12:42539580-42539730	GM12871	blood:	n/a	n/a
2	POLR2A	chr12:42538251-42539718	PBDE	blood:	n/a	n/a
3	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
4	CTCF	chr12:42539480-42539630	GM12868	blood:	n/a	n/a
5	POLR2A	chr12:42538439-42539671	K562	blood:	n/a	n/a
6	CTCF	chr12:42539580-42539730	HMEC	breast:	n/a	n/a
7	CTCF	chr12:42539520-42539670	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr12:42539520-42539670	A549	lung:	n/a	n/a
9	CTCF	chr12:42539540-42539690	HCT-116	colon:	n/a	n/a
10	CTCF	chr12:42539520-42539670	RPTEC	kidney:	n/a	n/a
11	POLR2A	chr12:42537845-42539754	Raji	blood:	n/a	n/a
12	MAX	chr12:42539518-42539697	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr12:42539520-42539694	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr12:42539537-42539685	MCF-7	breast:	n/a	n/a
15	EGR1	chr12:42539297-42539603	K562	blood:	n/a	chr12:42539471-42539485 chr12:42539474-42539483 chr12:42539471-42539484 chr12:42539472-42539483 chr12:42539473-42539483 chr12:42539471-42539484 chr12:42539471-42539484 chr12:42539473-42539483
16	CBX3	chr12:42538497-42539742	K562	blood:	n/a	n/a
17	CTCF	chr12:42539516-42539703	MCF-7	breast:	n/a	n/a
18	MTA3	chr12:42538490-42539603	GM12878	blood:	n/a	n/a
19	CTCF	chr12:42539597-42539636	Medullo	brain:	n/a	n/a
20	RCOR1	chr12:42538467-42539795	K562	blood:	n/a	n/a
21	TEAD4	chr12:42538400-42539740	K562	blood:	n/a	n/a
22	CTCF	chr12:42539557-42539666	HUVEC	blood vessel:	n/a	n/a
23	CTCF	chr12:42539480-42539630	GM12873	blood:	n/a	n/a
24	CTCF	chr12:42539500-42539650	HCPEpiC	choroid plexus:	n/a	n/a
25	MXI1	chr12:42536964-42539693	SK-N-SH	brain:	n/a	n/a
26	NR3C1	chr12:42539369-42539805	A549	lung:	n/a	chr12:42539568-42539582 chr12:42539568-42539582 chr12:42539565-42539586 chr12:42539567-42539584
27	CTCF	chr12:42539480-42539630	GM12864	blood:	n/a	n/a
28	JUND	chr12:42538117-42539779	K562	blood:	n/a	n/a
29	POLR2A	chr12:42538078-42539725	NB4	blood:	n/a	n/a
30	TCF12	chr12:42538262-42539894	A549	lung:	n/a	chr12:42539655-42539663
31	CTCF	chr12:42539540-42539690	MCF-7	breast:	n/a	n/a
32	CTCF	chr12:42539500-42539650	NB4	blood:	n/a	n/a
33	WRNIP1	chr12:42538635-42540104	GM12878	blood:	n/a	n/a
34	RAD21	chr12:42539321-42539809	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr12:42539441-42539717	A549	lung:	n/a	n/a
36	RAD21	chr12:42539476-42539838	A549	lung:	n/a	n/a
37	CTCF	chr12:42539560-42539710	Caco-2	colon:	n/a	n/a
38	KAP1	chr12:42538386-42539924	HEK293	kidney:	n/a	n/a
39	EGR1	chr12:42539331-42539655	K562	blood:	n/a	chr12:42539471-42539485 chr12:42539474-42539483 chr12:42539471-42539484 chr12:42539472-42539483 chr12:42539473-42539483 chr12:42539471-42539484 chr12:42539471-42539484 chr12:42539473-42539483
40	CTCF	chr12:42539439-42539709	A549	lung:	n/a	n/a
41	CTCF	chr12:42539544-42539680	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr12:42539480-42539630	HBMEC	blood vessel:	n/a	n/a
43	CTCF	chr12:42539480-42539630	HMEC	breast:	n/a	n/a
44	MAZ	chr12:42537925-42539956	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
45	CTCF	chr12:42539592-42539659	GM13977	blood:	n/a	n/a
46	CTCF	chr12:42539500-42539650	GM12874	blood:	n/a	n/a
47	CTCF	chr12:42539520-42539670	SAEC	small airway:	n/a	n/a
48	CTCF	chr12:42539540-42539690	HEK293	kidney:	n/a	n/a
49	FOXA1	chr12:42539226-42539762	A549	lung:	n/a	n/a
50	MYC	chr12:42537683-42539853	NB4	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519

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
ENSG00000139168	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000269367	Chromatin interaction

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

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

rs_ID	r²[population]
rs10880255	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]
rs11181340	0.90[ASN][1000 genomes]
rs11181341	0.90[ASN][1000 genomes]
rs11181363	0.94[CHB][hapmap];0.84[JPT][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap]
rs7135955	1.00[CHB][hapmap];0.82[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42537000-42539600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:42537400-42539600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:42537400-42539600	Active TSS	Colonic Mucosa	Colon
4	chr12:42537400-42540000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:42537800-42539600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:42537800-42539600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:42537800-42539600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:42538000-42539600	Active TSS	Stomach Smooth Muscle	stomach
9	chr12:42538600-42539600	Flanking Bivalent TSS/Enh	Dnd41	blood
10	chr12:42538800-42539600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:42538800-42539600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:42538800-42539600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:42538800-42539600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:42538800-42539600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr12:42538800-42539600	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:42538800-42539800	Flanking Active TSS	K562	blood
17	chr12:42539000-42539600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr12:42539000-42539600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:42539000-42539600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:42539000-42539600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:42539000-42539600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:42539000-42539600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr12:42539000-42539600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr12:42539000-42539600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:42539000-42539600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:42539000-42539600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr12:42539000-42539600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr12:42539000-42539600	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr12:42539000-42539600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:42539000-42539600	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr12:42539000-42539600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr12:42539000-42539600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:42539000-42539600	Flanking Active TSS	HepG2	liver
34	chr12:42539000-42539800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:42539000-42539800	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr12:42539000-42540000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr12:42539200-42539600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:42539200-42539600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:42539200-42539600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:42539200-42539600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
41	chr12:42539200-42539600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:42539200-42539600	Active TSS	Primary hematopoietic stem cells	blood
43	chr12:42539200-42539600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:42539200-42539600	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr12:42539200-42539600	Enhancers	Fetal Thymus	thymus
46	chr12:42539200-42539600	Flanking Active TSS	Pancreas	Pancrea
47	chr12:42539200-42539600	Enhancers	Psoas Muscle	Psoas
48	chr12:42539200-42539600	Enhancers	HSMMtube	muscle
49	chr12:42539200-42539800	Enhancers	Esophagus	oesophagus
50	chr12:42539200-42539800	Enhancers	Fetal Muscle Leg	muscle

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