Variant report

Variant	rs5998086
Chromosome Location	chr22:32080244-32080245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10154390	0.84[EUR][1000 genomes]
rs12165432	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12171042	0.83[ASW][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap]
rs12627933	0.83[MEX][hapmap]
rs131221	0.81[AFR][1000 genomes]
rs131225	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131233	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131244	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs131245	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs131250	0.88[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs131253	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs140078	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]
rs140081	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]
rs2006771	0.86[YRI][hapmap]
rs2092905	0.83[MEX][hapmap]
rs2108108	0.94[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs2236033	0.83[MEX][hapmap]
rs2295251	0.89[MEX][hapmap]
rs28528942	0.86[ASN][1000 genomes]
rs3804087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818134	0.84[MEX][hapmap]
rs4820979	0.84[MEX][hapmap]
rs4820980	0.84[MEX][hapmap]
rs5749306	0.83[MEX][hapmap]
rs5753667	0.84[MEX][hapmap]
rs5753691	0.81[MEX][hapmap]
rs5753734	0.83[ASW][hapmap];0.89[MEX][hapmap]
rs5994419	0.81[AFR][1000 genomes]
rs5994420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5994427	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs5994431	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap]
rs5998054	0.83[MEX][hapmap]
rs5998069	0.82[MEX][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap]
rs5998072	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5998119	0.86[ASN][1000 genomes]
rs5998136	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap]
rs62238892	0.86[ASN][1000 genomes]
rs7287937	0.89[YRI][hapmap]
rs7289075	0.86[YRI][hapmap]
rs7290856	0.89[GIH][hapmap]
rs7291918	0.83[ASW][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap]
rs738656	0.84[MEX][hapmap]
rs738684	0.83[MEX][hapmap]
rs760908	0.89[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs761746	0.89[MEX][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap]
rs8141214	0.94[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs8461	0.89[MEX][hapmap]
rs9621327	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9956	0.82[ASW][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5998086	ZNRF3	cis	parietal	SCAN
rs5998086	TTC28AS	cis	cerebellum	SCAN
rs5998086	TCN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32068400-32080400	Weak transcription	Hela-S3	cervix
2	chr22:32072600-32080600	Weak transcription	Fetal Heart	heart
3	chr22:32072600-32081000	Weak transcription	Aorta	Aorta
4	chr22:32073200-32080800	Weak transcription	Stomach Mucosa	stomach
5	chr22:32073200-32080800	Weak transcription	A549	lung
6	chr22:32073200-32087200	Weak transcription	Fetal Kidney	kidney
7	chr22:32073200-32089000	Weak transcription	Fetal Brain Male	brain
8	chr22:32073200-32091200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:32073200-32098600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr22:32073400-32081000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr22:32073400-32081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr22:32073400-32088200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr22:32073400-32088400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr22:32073400-32088400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr22:32073400-32111800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr22:32074400-32100400	Weak transcription	K562	blood
17	chr22:32076000-32080400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr22:32076200-32080600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr22:32076600-32107600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr22:32077200-32082800	Weak transcription	Right Atrium	heart
21	chr22:32077200-32108000	Weak transcription	Psoas Muscle	Psoas
22	chr22:32077200-32109200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr22:32077800-32080400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr22:32077800-32084400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr22:32077800-32088400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:32078000-32085600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:32078000-32088200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr22:32078000-32088400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr22:32078000-32111400	Strong transcription	Fetal Intestine Small	intestine
30	chr22:32078200-32082000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr22:32078200-32084400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:32078200-32088600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr22:32078200-32093200	Strong transcription	Fetal Intestine Large	intestine
34	chr22:32078400-32091400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr22:32078400-32093800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr22:32078400-32101200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:32078400-32101200	Strong transcription	Placenta	Placenta
38	chr22:32078400-32111800	Strong transcription	Fetal Stomach	stomach
39	chr22:32078600-32081800	Strong transcription	Colonic Mucosa	Colon
40	chr22:32078600-32082200	Strong transcription	Spleen	Spleen
41	chr22:32078600-32082800	Strong transcription	Brain Germinal Matrix	brain
42	chr22:32078600-32082800	Strong transcription	Right Ventricle	heart
43	chr22:32078600-32083400	Strong transcription	Primary T cells from cord blood	blood
44	chr22:32078600-32083400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr22:32078600-32083600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr22:32078600-32083800	Strong transcription	Lung	lung
47	chr22:32078600-32084400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr22:32078600-32085000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr22:32078600-32085000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr22:32078600-32085200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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