Variant report

Variant	rs2858753
Chromosome Location	chr22:32351105-32351106
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:32350878..32354651-chr22:32358565..32361250,3	K562	blood:
2	chr22:32242768..32244279-chr22:32349703..32352012,2	K562	blood:
3	chr22:32346636..32349380-chr22:32349950..32352854,3	K562	blood:

Variant related genes	Relation type
ENSG00000100150	Chromatin interaction
ENSG00000227519	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1049583	0.89[CHB][hapmap]
rs12168840	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs130262	1.00[CEU][hapmap]
rs130266	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs13055495	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13057194	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs135021	1.00[CEU][hapmap]
rs135023	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs135110	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs135111	0.81[CEU][hapmap]
rs1807550	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1810413	0.82[AFR][1000 genomes]
rs1986211	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2246704	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301415	0.89[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs2413061	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2853884	0.86[CHB][hapmap]
rs2853887	0.86[CHB][hapmap]
rs2858750	0.89[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs2858752	0.89[CHB][hapmap]
rs3747158	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820059	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4820065	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4821004	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753852	0.90[CEU][hapmap]
rs5994457	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5994458	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5994461	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5998196	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5998198	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5998201	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5998204	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998233	0.81[CEU][hapmap]
rs5998237	0.81[CEU][hapmap]
rs8137665	0.81[CEU][hapmap]
rs8141011	0.89[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs8142505	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs93108	1.00[CEU][hapmap]
rs9606906	0.81[CEU][hapmap]
rs9609394	0.89[CHB][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	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2858753	CHEK2	cis	cerebellum	SCAN
rs2858753	LARGE	cis	cerebellum	SCAN
rs2858753	RHBDD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32342000-32354400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:32342400-32357600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32343400-32355000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:32343600-32354600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:32344600-32352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:32344800-32352000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:32345600-32351200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr22:32345600-32351200	Genic enhancers	Fetal Brain Female	brain
9	chr22:32345800-32351400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:32345800-32352600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr22:32346400-32351200	Genic enhancers	Rectal Mucosa Donor 31	rectum
12	chr22:32346600-32351200	Enhancers	Brain Anterior Caudate	brain
13	chr22:32346600-32351600	Enhancers	HUVEC	blood vessel
14	chr22:32346600-32352200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:32346600-32352800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr22:32346600-32356400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr22:32346800-32351200	Enhancers	Adipose Nuclei	Adipose
18	chr22:32346800-32351200	Enhancers	Stomach Mucosa	stomach
19	chr22:32346800-32351400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr22:32346800-32351400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr22:32346800-32352200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr22:32346800-32354800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:32347000-32351200	Enhancers	Thymus	Thymus
24	chr22:32347200-32351200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr22:32347200-32351200	Enhancers	Rectal Smooth Muscle	rectum
26	chr22:32347200-32355000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr22:32347400-32351200	Enhancers	Fetal Thymus	thymus
28	chr22:32347400-32351200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr22:32347400-32351400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr22:32347400-32351400	Enhancers	Fetal Heart	heart
31	chr22:32347400-32352200	Weak transcription	Fetal Kidney	kidney
32	chr22:32347400-32352400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr22:32347600-32352000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:32347600-32353000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr22:32347800-32351200	Enhancers	Psoas Muscle	Psoas
36	chr22:32348000-32351600	Weak transcription	Placenta	Placenta
37	chr22:32348000-32352000	Weak transcription	Colonic Mucosa	Colon
38	chr22:32348200-32351400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:32348200-32352200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:32348200-32352200	Weak transcription	Esophagus	oesophagus
41	chr22:32348200-32352400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:32348200-32352600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr22:32348400-32353200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr22:32348400-32354800	Strong transcription	Dnd41	blood
45	chr22:32348600-32351200	Genic enhancers	Osteobl	bone
46	chr22:32348600-32353600	Strong transcription	GM12878-XiMat	blood
47	chr22:32348800-32351400	Enhancers	Brain Angular Gyrus	brain
48	chr22:32348800-32352000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr22:32348800-32354200	Strong transcription	K562	blood
50	chr22:32348800-32355000	Strong transcription	Primary B cells from peripheral blood	blood

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