Variant report

Variant	rs3804085
Chromosome Location	chr22:31302233-31302234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31302112..31304619-chr22:31311790..31314732,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1003480	0.82[YRI][hapmap]
rs1005252	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs10854601	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11089481	0.85[MEX][hapmap]
rs11089484	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12166294	0.83[AMR][1000 genomes]
rs12167144	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12168307	0.85[AMR][1000 genomes]
rs1807686	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2016654	0.93[EUR][1000 genomes]
rs2019171	0.80[AFR][1000 genomes]
rs2019182	0.83[EUR][1000 genomes]
rs2072132	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2074578	0.83[ASW][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs2079221	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240175	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240176	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs2240177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240179	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240180	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240182	0.83[ASW][hapmap];0.96[YRI][hapmap]
rs2240183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2285918	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs3747151	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804084	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827330	0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3948685	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4820916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820921	0.80[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4820923	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4820925	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4820926	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5749185	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749186	0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs5749189	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749192	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749194	0.86[AFR][1000 genomes]
rs5749195	0.81[AFR][1000 genomes]
rs5749199	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749201	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753369	0.90[YRI][hapmap]
rs5753378	0.82[AMR][1000 genomes]
rs5753379	0.82[AMR][1000 genomes]
rs5753383	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753386	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753388	0.83[AFR][1000 genomes]
rs5753389	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753394	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753396	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753398	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs5753407	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753408	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753410	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5997802	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs5997807	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997830	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997838	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997846	0.93[YRI][hapmap]
rs6518726	0.85[EUR][1000 genomes]
rs6518729	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs722683	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs722684	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7284767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7289831	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7290078	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7291077	0.80[AFR][1000 genomes]
rs7291199	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7291361	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7291471	0.81[EUR][1000 genomes]
rs737924	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737926	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737927	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs739896	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8004	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8135974	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9609183	0.95[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9609185	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9609188	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9609193	0.83[EUR][1000 genomes]

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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3804085	MORC2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs3804085	C22orf27	cis	cerebellum	SCAN
rs3804085	MORC2-AS1	cis	Thyroid	GTEx
rs3804085	TUG1	Cis_1M	lymphoblastoid	RTeQTL
rs3804085	MORC2	cis	parietal	SCAN
rs3804085	MORC2-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31274200-31308400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr22:31278600-31321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31283000-31306600	Weak transcription	Fetal Heart	heart
4	chr22:31283400-31304000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr22:31283600-31318400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:31284400-31308400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:31284800-31306600	Weak transcription	Colonic Mucosa	Colon
8	chr22:31286400-31304000	Weak transcription	Ovary	ovary
9	chr22:31288400-31316400	Weak transcription	Thymus	Thymus
10	chr22:31290000-31305200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr22:31290000-31305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:31290200-31303800	Weak transcription	Gastric	stomach
13	chr22:31290200-31305000	Weak transcription	Pancreas	Pancrea
14	chr22:31290200-31308400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr22:31290400-31316600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr22:31290600-31316200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr22:31290800-31320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr22:31291000-31316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr22:31291200-31302600	Weak transcription	K562	blood
20	chr22:31291200-31316200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr22:31291400-31315400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr22:31293800-31310200	Weak transcription	Hela-S3	cervix
23	chr22:31294200-31302400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr22:31294800-31309400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr22:31295400-31321000	Weak transcription	HSMMtube	muscle
26	chr22:31296200-31309000	Weak transcription	Left Ventricle	heart
27	chr22:31296400-31302600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:31296800-31310600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:31297000-31305600	Strong transcription	Fetal Intestine Small	intestine
30	chr22:31297400-31309400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr22:31298200-31305800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr22:31298400-31303000	Strong transcription	Fetal Brain Female	brain
33	chr22:31298400-31306600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:31298600-31304600	Strong transcription	Fetal Stomach	stomach
35	chr22:31298800-31303800	Weak transcription	Brain Germinal Matrix	brain
36	chr22:31299000-31303600	Weak transcription	HSMM	muscle
37	chr22:31299200-31309800	Weak transcription	Primary B cells from cord blood	blood
38	chr22:31299600-31303800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr22:31299600-31304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:31299600-31308800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr22:31299600-31316600	Weak transcription	NHEK	skin
42	chr22:31299800-31304000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr22:31299800-31305000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr22:31299800-31307600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr22:31299800-31317000	Weak transcription	Brain Angular Gyrus	brain
46	chr22:31300000-31307200	Weak transcription	GM12878-XiMat	blood
47	chr22:31300200-31302400	Weak transcription	Fetal Brain Male	brain
48	chr22:31300200-31303800	Weak transcription	Lung	lung
49	chr22:31300200-31304000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:31300200-31304000	Weak transcription	Primary T cells from cord blood	blood

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