Variant report

Variant	rs10744538
Chromosome Location	chr12:279586-279587
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	TCF12	chr12:279384-280044	ECC-1	luminal epithelium:	n/a	chr12:279636-279646
2	BACH1	chr12:279583-279884	H1-hESC	embryonic stem cell:	n/a	n/a
3	EP300	chr12:279218-280049	ECC-1	luminal epithelium:	n/a	chr12:279455-279462

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:278455..281013-chr12:283457..285093,2	K562	blood:
2	chr12:276004..278175-chr12:278500..282427,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256694	TF binding region
ENSG00000120645	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10505717	0.94[ASN][1000 genomes]
rs10773937	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10848481	0.84[ASN][1000 genomes]
rs11061708	0.86[ASN][1000 genomes]
rs11061709	0.94[ASN][1000 genomes]
rs12368193	0.84[ASN][1000 genomes]
rs17692962	0.95[ASN][1000 genomes]
rs183355	0.85[ASN][1000 genomes]
rs216227	0.85[ASN][1000 genomes]
rs2291917	0.84[ASN][1000 genomes]
rs2291918	0.92[ASN][1000 genomes]
rs2291919	0.87[ASN][1000 genomes]
rs2291920	0.94[ASN][1000 genomes]
rs3892665	0.84[ASN][1000 genomes]
rs502783	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs505387	0.85[ASN][1000 genomes]
rs559759	0.80[JPT][hapmap]
rs565091	0.81[ASN][1000 genomes]
rs57052808	0.86[ASN][1000 genomes]
rs61907087	0.83[ASN][1000 genomes]
rs61907088	0.83[ASN][1000 genomes]
rs633159	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7959974	0.85[CHD][hapmap]
rs7960096	0.85[CHD][hapmap]
rs7967899	0.84[ASN][1000 genomes]
rs7967909	0.83[ASN][1000 genomes]
rs7971499	0.85[ASN][1000 genomes]
rs797736	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983433	chr12:145740-400932	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv427901	chr12:146333-344299	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv428269	chr12:146333-344299	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1041243	chr12:150430-310571	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038621	chr12:150430-324923	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv898552	chr12:154752-303320	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10744538	PARP11	cis	cerebellum	SCAN
rs10744538	IQSEC3	cis	parietal	SCAN
rs10744538	ZSCAN18	trans	parietal	SCAN
rs10744538	ITFG2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:249000-284200	Weak transcription	Right Atrium	heart
2	chr12:253800-285600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:262800-284200	Weak transcription	Brain Angular Gyrus	brain
4	chr12:266200-280000	Weak transcription	Right Ventricle	heart
5	chr12:268800-284200	Weak transcription	Brain Anterior Caudate	brain
6	chr12:273000-281000	Weak transcription	Colonic Mucosa	Colon
7	chr12:273600-284600	Weak transcription	Esophagus	oesophagus
8	chr12:276200-282800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:276200-284000	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:276400-280200	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr12:276400-281000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:276400-283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:276600-279800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr12:277200-292800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:277400-280200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr12:277400-283200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:277600-280000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr12:277600-280800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:277600-280800	Weak transcription	Stomach Mucosa	stomach
20	chr12:277600-281000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr12:277800-279800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:277800-279800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr12:277800-280000	Enhancers	NH-A	brain
24	chr12:277800-280800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:277800-282400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:278400-280000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:278400-280600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:278400-283400	Weak transcription	Liver	Liver
29	chr12:278400-283600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:278400-288400	Weak transcription	Fetal Kidney	kidney
31	chr12:278600-279600	Weak transcription	Fetal Brain Female	brain
32	chr12:278600-280000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:278600-280400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:278600-280800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr12:278600-281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:278600-281000	Weak transcription	Left Ventricle	heart
37	chr12:278600-282200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr12:278600-283400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:278800-280600	Weak transcription	Fetal Stomach	stomach
40	chr12:278800-280800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:279000-279800	Enhancers	Fetal Lung	lung
42	chr12:279000-280000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:279000-280600	Weak transcription	Fetal Heart	heart
44	chr12:279000-281200	Weak transcription	Fetal Intestine Large	intestine
45	chr12:279000-285200	Weak transcription	Fetal Thymus	thymus
46	chr12:279200-281000	Weak transcription	HSMM	muscle
47	chr12:279400-279800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:279400-280000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:279400-280200	Bivalent Enhancer	Placenta	Placenta
50	chr12:279400-280600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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