Variant report

Variant	rs140078
Chromosome Location	chr22:32110163-32110164
allele	A/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	POLR2A	chr22:32107803-32112712	K562	blood:	n/a	n/a
2	MXI1	chr22:32110151-32112213	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PRR14L	TF binding region

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	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12171042	0.83[ASW][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs12627933	0.82[MEX][hapmap]
rs131221	0.86[AFR][1000 genomes]
rs131225	0.98[AFR][1000 genomes];0.97[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];0.96[AFR][1000 genomes];0.97[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];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs131245	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[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];0.88[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs131253	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs140081	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];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs2236033	0.82[MEX][hapmap]
rs2295251	0.89[MEX][hapmap]
rs28528942	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];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818134	0.84[MEX][hapmap]
rs4820979	0.84[MEX][hapmap]
rs4820980	0.84[MEX][hapmap]
rs5749306	0.82[MEX][hapmap]
rs5753691	0.81[MEX][hapmap]
rs5753734	0.83[ASW][hapmap];0.89[MEX][hapmap]
rs5994420	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[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];0.95[ASN][1000 genomes]
rs5994431	0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap]
rs5998054	0.82[MEX][hapmap]
rs5998069	0.82[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs5998072	0.91[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];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[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];0.82[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];0.83[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs738656	0.84[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];0.91[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs761746	0.89[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap]
rs8141214	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs8461	0.89[MEX][hapmap]
rs9621327	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9956	0.82[ASW][hapmap];0.89[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
rs140078	ZNRF3	cis	parietal	SCAN
rs140078	TCN2	cis	cerebellum	SCAN
rs140078	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32073400-32111800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:32078000-32111400	Strong transcription	Fetal Intestine Small	intestine
3	chr22:32078400-32111800	Strong transcription	Fetal Stomach	stomach
4	chr22:32078800-32126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:32079000-32113800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr22:32080400-32121400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr22:32081200-32126400	Weak transcription	Stomach Mucosa	stomach
8	chr22:32081600-32110600	Weak transcription	Hela-S3	cervix
9	chr22:32089200-32113800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr22:32089400-32126000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr22:32092000-32113800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr22:32095400-32113400	Strong transcription	Fetal Intestine Large	intestine
13	chr22:32098600-32111600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:32099600-32111400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:32101000-32110200	Weak transcription	Fetal Heart	heart
16	chr22:32101000-32110400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr22:32101200-32110400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr22:32101200-32110400	Weak transcription	HUVEC	blood vessel
19	chr22:32102800-32112200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr22:32102800-32123000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr22:32103000-32125000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr22:32103200-32113400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr22:32103200-32113600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:32103600-32113400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr22:32103600-32113600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:32103800-32111400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:32103800-32113800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr22:32104400-32113400	Strong transcription	Fetal Muscle Leg	muscle
29	chr22:32104400-32113600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr22:32104400-32113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:32104400-32113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:32104400-32114200	Strong transcription	Thymus	Thymus
33	chr22:32104600-32113400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr22:32104600-32113600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:32104600-32113800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr22:32104600-32114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:32105000-32121400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:32105000-32124000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:32105000-32124200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr22:32105200-32113400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr22:32105200-32113400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr22:32105200-32113600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr22:32105200-32113600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr22:32105200-32114200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:32105200-32123600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:32105400-32124200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:32105600-32113400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr22:32105800-32113200	Strong transcription	Adipose Nuclei	Adipose
49	chr22:32105800-32113600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr22:32105800-32113600	Strong transcription	Liver	Liver

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