Variant report

Variant	rs738987
Chromosome Location	chr22:34288977-34288978
allele	A/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	CEBPB	chr22:34288655-34289018	HepG2	liver:	n/a	chr22:34288830-34288841 chr22:34288829-34288840

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34287867..34289464-chr22:34291655..34293352,2	MCF-7	breast:

Variant related genes	Relation type
LARGE	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1005680	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483174	1.00[ASN][1000 genomes]
rs11703305	1.00[ASN][1000 genomes]
rs11704212	1.00[ASN][1000 genomes]
rs11705063	1.00[ASN][1000 genomes]
rs11912301	1.00[ASN][1000 genomes]
rs11912405	1.00[ASN][1000 genomes]
rs11913804	1.00[ASN][1000 genomes]
rs11914012	1.00[ASN][1000 genomes]
rs130523	1.00[ASN][1000 genomes]
rs13055480	1.00[ASN][1000 genomes]
rs16993078	1.00[ASN][1000 genomes]
rs16993089	1.00[ASN][1000 genomes]
rs17747599	1.00[ASN][1000 genomes]
rs2157153	0.85[CEU][hapmap]
rs2213360	0.81[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2267315	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2267316	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2283957	0.89[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2283959	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2413206	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413207	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2413208	1.00[ASN][1000 genomes]
rs34060203	1.00[ASN][1000 genomes]
rs34290110	1.00[ASN][1000 genomes]
rs34375307	1.00[ASN][1000 genomes]
rs34455747	1.00[ASN][1000 genomes]
rs34597805	1.00[ASN][1000 genomes]
rs34871405	1.00[ASN][1000 genomes]
rs35838699	1.00[ASN][1000 genomes]
rs36006309	1.00[ASN][1000 genomes]
rs3919426	0.84[EUR][1000 genomes]
rs55819147	1.00[ASN][1000 genomes]
rs55963330	1.00[ASN][1000 genomes]
rs5749689	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749698	1.00[ASN][1000 genomes]
rs5754739	0.93[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754746	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754748	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58634529	1.00[ASN][1000 genomes]
rs5999089	1.00[ASN][1000 genomes]
rs67258059	1.00[ASN][1000 genomes]
rs73154536	1.00[ASN][1000 genomes]
rs73154574	1.00[ASN][1000 genomes]
rs73170572	1.00[ASN][1000 genomes]
rs73170587	1.00[ASN][1000 genomes]
rs73170592	1.00[ASN][1000 genomes]
rs73170593	1.00[ASN][1000 genomes]
rs73170600	1.00[ASN][1000 genomes]
rs73171909	1.00[ASN][1000 genomes]
rs73171910	1.00[ASN][1000 genomes]
rs73171912	1.00[ASN][1000 genomes]
rs73171913	1.00[ASN][1000 genomes]
rs73171915	1.00[ASN][1000 genomes]
rs73171921	1.00[ASN][1000 genomes]
rs73171926	1.00[ASN][1000 genomes]
rs73171927	1.00[ASN][1000 genomes]
rs73171931	1.00[ASN][1000 genomes]
rs738989	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933215	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv588938	chr22:34270568-34307875	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs738987	C22orf24	cis	cerebellum	SCAN
rs738987	TMEM41A	trans	cerebellum	SCAN
rs738987	HMGXB4	cis	parietal	SCAN
rs738987	SMTN	cis	parietal	SCAN
rs738987	TOM1	cis	parietal	SCAN
rs738987	ASCC2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34273200-34292200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr22:34274600-34291200	Enhancers	Fetal Heart	heart
3	chr22:34280000-34292200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:34280600-34289200	Weak transcription	Stomach Mucosa	stomach
5	chr22:34280800-34293200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:34281000-34289800	Weak transcription	Pancreas	Pancrea
7	chr22:34281200-34289800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr22:34283000-34292000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr22:34285000-34292400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr22:34285400-34290800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr22:34285600-34290600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr22:34286000-34290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr22:34286000-34291800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:34286200-34289200	Weak transcription	Fetal Brain Female	brain
15	chr22:34286200-34290400	Weak transcription	Esophagus	oesophagus
16	chr22:34286400-34290600	Weak transcription	Colon Smooth Muscle	Colon
17	chr22:34286400-34290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr22:34286400-34292200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr22:34286400-34296600	Weak transcription	Adipose Nuclei	Adipose
20	chr22:34286800-34290600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr22:34287000-34289800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr22:34287000-34290800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:34287200-34289800	Weak transcription	Left Ventricle	heart
24	chr22:34287200-34289800	Weak transcription	Right Ventricle	heart
25	chr22:34287200-34291400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr22:34287400-34294400	Weak transcription	Fetal Brain Male	brain
27	chr22:34287800-34298600	Enhancers	H9 Cell Line	embryonic stem cell
28	chr22:34287800-34299000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr22:34288000-34290000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr22:34288200-34290800	Enhancers	Liver	Liver
31	chr22:34288200-34295000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr22:34288200-34303000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr22:34288400-34289800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr22:34288400-34289800	Weak transcription	Gastric	stomach
35	chr22:34288600-34290000	Weak transcription	Psoas Muscle	Psoas
36	chr22:34288600-34291200	Enhancers	HepG2	liver
37	chr22:34288600-34293000	Weak transcription	Fetal Lung	lung
38	chr22:34288800-34290200	Weak transcription	Right Atrium	heart
39	chr22:34288800-34290400	Weak transcription	Brain Anterior Caudate	brain
40	chr22:34288800-34291000	Enhancers	Fetal Intestine Small	intestine
41	chr22:34288800-34292400	Weak transcription	Ovary	ovary
42	chr22:34288800-34292800	Enhancers	HUES64 Cell Line	embryonic stem cell

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