Variant report

Variant	rs5752887
Chromosome Location	chr22:29641018-29641019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29598605..29599258-chr22:29640938..29642145,5	MCF-7	breast:
2	chr22:29598263..29599277-chr22:29640793..29642655,17	MCF-7	breast:
3	chr22:29639575..29642447-chr22:29663605..29665406,2	K562	blood:
4	chr22:29640165..29643423-chr22:29644673..29648917,5	K562	blood:
5	chr22:29640909..29643283-chr22:29659870..29662528,2	K562	blood:
6	chr22:29473166..29474828-chr22:29640994..29643456,2	K562	blood:

Variant related genes	Relation type
ENSG00000100263	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12166644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12628709	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16987313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765295	0.94[ASN][1000 genomes]
rs3765297	0.96[ASN][1000 genomes]
rs3765300	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3950176	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752884	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752888	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752889	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752895	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763080	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5763084	1.00[ASN][1000 genomes]
rs5763087	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763091	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763092	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763094	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763105	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763110	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763111	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6006068	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6006072	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006073	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006074	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv275243	chr22:29638470-29642365	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5752887	TMEM211	cis	parietal	SCAN
rs5752887	PIWIL3	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29622000-29655200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29622000-29655800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:29622400-29656600	Weak transcription	Colonic Mucosa	Colon
4	chr22:29622600-29641400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:29628400-29641200	Weak transcription	Fetal Brain Male	brain
6	chr22:29629000-29659400	Weak transcription	Brain Anterior Caudate	brain
7	chr22:29629600-29655400	Weak transcription	Liver	Liver
8	chr22:29629600-29655400	Weak transcription	Gastric	stomach
9	chr22:29630200-29641400	Weak transcription	Pancreas	Pancrea
10	chr22:29633600-29654400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr22:29634600-29655200	Weak transcription	Brain Angular Gyrus	brain
12	chr22:29634800-29641200	Strong transcription	Fetal Intestine Large	intestine
13	chr22:29638400-29655200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr22:29638600-29641200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr22:29638800-29641200	Strong transcription	Fetal Lung	lung
16	chr22:29639000-29641200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:29639000-29641200	Strong transcription	Fetal Intestine Small	intestine
18	chr22:29639000-29655200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr22:29639200-29643200	Strong transcription	Fetal Stomach	stomach
20	chr22:29639400-29654200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr22:29639600-29642000	Genic enhancers	Dnd41	blood
22	chr22:29639800-29641400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr22:29639800-29641600	Enhancers	Thymus	Thymus
24	chr22:29639800-29642000	Enhancers	Fetal Thymus	thymus
25	chr22:29639800-29656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:29640000-29641400	Weak transcription	Ovary	ovary
27	chr22:29640200-29641400	Weak transcription	Fetal Muscle Leg	muscle
28	chr22:29640200-29650200	Weak transcription	Brain Germinal Matrix	brain
29	chr22:29640400-29641200	Weak transcription	Fetal Brain Female	brain
30	chr22:29640400-29641400	Weak transcription	GM12878-XiMat	blood
31	chr22:29640400-29641800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr22:29640400-29642000	Weak transcription	Fetal Kidney	kidney
33	chr22:29640400-29651200	Weak transcription	Lung	lung
34	chr22:29640800-29641600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr22:29640800-29641600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr22:29640800-29641600	Genic enhancers	Spleen	Spleen
37	chr22:29641000-29641200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:29641000-29641600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:29641000-29641800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:29641000-29642600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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