Variant report

Variant	rs140081
Chromosome Location	chr22:32112461-32112462
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	POLR2A	chr22:32107803-32112712	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	22:31836635-31847259..22:32110635-32115702	Hela-S3	cervix:
2	22:32110635-32115702..22:32860159-32865649	K562	blood:
3	22:32110635-32115702..22:32170492-32188129	GM12878	blood:
4	chr22:32110777..32113551-chr22:32120326..32122209,2	MCF-7	breast:
5	22:32110635-32115702..22:32342898-32343477	GM12878	blood:

Variant related genes	Relation type
PRR14L	TF binding region
ENSG00000100150	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000128245	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10154390	0.81[EUR][1000 genomes]
rs12165432	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12171042	0.83[ASW][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs12627933	0.82[MEX][hapmap]
rs131221	0.87[AFR][1000 genomes]
rs131225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs131233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131244	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs131245	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs131250	0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs131253	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs140078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006771	0.86[YRI][hapmap]
rs2092905	0.82[MEX][hapmap]
rs2108108	0.87[CHB][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs2236033	0.82[MEX][hapmap]
rs2295251	0.88[MEX][hapmap]
rs28528942	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3804087	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818134	0.83[MEX][hapmap]
rs4820979	0.83[MEX][hapmap]
rs4820980	0.83[MEX][hapmap]
rs5749306	0.82[MEX][hapmap]
rs5753691	0.87[MEX][hapmap]
rs5753734	0.83[ASW][hapmap];0.88[MEX][hapmap]
rs5994420	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5994427	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5994431	0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap]
rs5998054	0.82[MEX][hapmap]
rs5998069	0.87[MEX][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap]
rs5998072	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5998086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5998119	0.89[ASN][1000 genomes]
rs5998121	0.81[ASN][1000 genomes]
rs5998122	0.81[ASN][1000 genomes]
rs5998136	0.87[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap];0.82[ASN][1000 genomes]
rs62238892	0.89[ASN][1000 genomes]
rs7287937	0.83[MKK][hapmap];0.89[YRI][hapmap]
rs7289075	0.86[YRI][hapmap]
rs7290856	0.88[GIH][hapmap]
rs7291918	0.83[ASW][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs738656	0.83[MEX][hapmap]
rs738684	0.82[MEX][hapmap]
rs760908	0.89[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs761746	0.88[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap]
rs8141214	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs8461	0.88[MEX][hapmap]
rs9621327	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9956	0.82[ASW][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060929	chr22:32102701-32176860	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs140081	ZNRF3	cis	parietal	SCAN
rs140081	TCN2	cis	cerebellum	SCAN
rs140081	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32078800-32126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr22:32079000-32113800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr22:32080400-32121400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr22:32081200-32126400	Weak transcription	Stomach Mucosa	stomach
5	chr22:32089200-32113800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:32089400-32126000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:32092000-32113800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr22:32095400-32113400	Strong transcription	Fetal Intestine Large	intestine
9	chr22:32102800-32123000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:32103000-32125000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr22:32103200-32113400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr22:32103200-32113600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:32103600-32113400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr22:32103600-32113600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr22:32103800-32113800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr22:32104400-32113400	Strong transcription	Fetal Muscle Leg	muscle
17	chr22:32104400-32113600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr22:32104400-32113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr22:32104400-32113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr22:32104400-32114200	Strong transcription	Thymus	Thymus
21	chr22:32104600-32113400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr22:32104600-32113600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr22:32104600-32113800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr22:32104600-32114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:32105000-32121400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr22:32105000-32124000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr22:32105000-32124200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr22:32105200-32113400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr22:32105200-32113400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr22:32105200-32113600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr22:32105200-32113600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:32105200-32114200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr22:32105200-32123600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:32105400-32124200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr22:32105600-32113400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr22:32105800-32113200	Strong transcription	Adipose Nuclei	Adipose
37	chr22:32105800-32113600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr22:32105800-32113600	Strong transcription	Liver	Liver
39	chr22:32105800-32113800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:32105800-32113800	Strong transcription	Fetal Brain Female	brain
41	chr22:32105800-32113800	Strong transcription	NHDF-Ad	bronchial
42	chr22:32105800-32123200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr22:32105800-32124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr22:32105800-32125000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr22:32106000-32113600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr22:32106000-32113600	Strong transcription	Dnd41	blood
47	chr22:32106000-32113800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr22:32106200-32113400	Strong transcription	NH-A	brain
49	chr22:32106200-32113600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr22:32106200-32113600	Strong transcription	HepG2	liver

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