Variant report

Variant	rs2283792
Chromosome Location	chr22:22131125-22131126
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:22130987..22131678-chr22:22292900..22293506,2	K562	blood:
2	chr22:22130737..22132240-chr22:22289657..22292393,2	K562	blood:
3	chr22:22130696..22132847-chr22:22280604..22282994,2	K562	blood:
4	chr22:22128103..22132629-chr22:22289657..22294176,6	K562	blood:
5	chr22:22130567..22133549-chr22:22209125..22210877,2	K562	blood:
6	chr22:22129393..22132158-chr22:22299862..22301892,2	K562	blood:

Variant related genes	Relation type
ENSG00000100034	Chromatin interaction
ENSG00000224086	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11704205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892846	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2006893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2266965	0.84[EUR][1000 genomes]
rs2266967	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283794	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2298432	0.82[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs240049	0.89[CEU][hapmap]
rs34550586	0.83[ASN][1000 genomes]
rs3788332	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810610	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4478016	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4516540	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4821402	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs5749806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749937	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749986	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749998	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5750113	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5754941	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5755099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5755694	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5999515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5999521	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5999550	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5999750	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6518986	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743409	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8136590	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8136867	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8141851	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9607287	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9607347	0.83[EUR][1000 genomes]
rs9610375	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs9610458	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
2	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
3	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
4	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
5	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
6	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
7	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
8	nsv1066403	chr22:22010822-22352262	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv510804	chr22:22024531-22132764	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1066964	chr22:22055123-22228745	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv544604	chr22:22055123-22228745	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3423141	chr22:22074283-22135439	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv588322	chr22:22086373-22186479	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv948580	chr22:22100718-22839559	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
15	esv1795495	chr22:22131125-22204916	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv914470	chr22:22131125-22272737	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1059265	chr22:22131125-22457154	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2283792	SCARF2	cis	parietal	SCAN
rs2283792	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs2283792	LL22NC03-86G7.1	cis	Whole Blood	GTEx
rs2283792	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx
rs2283792	PPM1F	cis	uninvolved skin	skin_eQTL
rs2283792	MAPK1	Cis_1M	lymphoblastoid	RTeQTL
rs2283792	MIF	cis	parietal	SCAN
rs2283792	DERL3	cis	cerebellum	SCAN
rs2283792	LL22NC03-86G7.1	cis	Adipose Subcutaneous	GTEx
rs2283792	psiTPTE22	cis	parietal	SCAN
rs2283792	LL22NC03-86G7.1	cis	Muscle Skeletal	GTEx
rs2283792	LL22NC03-86G7.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2283792	LL22NC03-86G7.1	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22110600-22150600	Weak transcription	Fetal Heart	heart
2	chr22:22112400-22136800	Strong transcription	Dnd41	blood
3	chr22:22113400-22163800	Weak transcription	Right Atrium	heart
4	chr22:22113600-22133200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:22114200-22172800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:22116000-22132800	Strong transcription	K562	blood
7	chr22:22118800-22133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr22:22121600-22171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:22122200-22132200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr22:22123200-22133600	Strong transcription	Thymus	Thymus
11	chr22:22123200-22162200	Strong transcription	Fetal Thymus	thymus
12	chr22:22127000-22139200	Weak transcription	Stomach Mucosa	stomach
13	chr22:22127200-22133000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr22:22127200-22134600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr22:22127200-22136200	Weak transcription	Pancreas	Pancrea
16	chr22:22127200-22138400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:22127200-22141000	Weak transcription	Aorta	Aorta
18	chr22:22127200-22142400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr22:22127200-22145200	Weak transcription	Small Intestine	intestine
20	chr22:22127200-22146000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
22	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
23	chr22:22127400-22131200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:22127400-22131200	Weak transcription	Placenta	Placenta
25	chr22:22127400-22131600	Weak transcription	NHEK	skin
26	chr22:22127400-22133000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr22:22127400-22133600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr22:22127400-22134600	Weak transcription	Fetal Brain Male	brain
29	chr22:22127400-22137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:22127400-22137800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr22:22127400-22138800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr22:22127400-22139000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr22:22127400-22141600	Weak transcription	Colonic Mucosa	Colon
34	chr22:22127400-22145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr22:22127400-22146000	Weak transcription	A549	lung
36	chr22:22127600-22132000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr22:22127600-22133600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr22:22127600-22136000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr22:22127600-22136400	Weak transcription	Esophagus	oesophagus
40	chr22:22128200-22136000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr22:22128600-22133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:22128600-22133000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:22128600-22133000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr22:22128600-22133000	Weak transcription	GM12878-XiMat	blood
45	chr22:22128600-22136000	Weak transcription	Gastric	stomach
46	chr22:22128600-22138800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:22128600-22139000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr22:22128800-22131800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr22:22129000-22162200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr22:22129600-22133000	Weak transcription	Brain Inferior Temporal Lobe	brain

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