Variant report

Variant	rs138631
Chromosome Location	chr22:28372834-28372835
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	chr22:28371840..28377290-chr22:28378156..28383171,5	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs118839	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12171034	0.82[ASN][1000 genomes]
rs138638	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs138650	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs138675	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs138683	0.82[ASN][1000 genomes]
rs138685	0.81[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1548235	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs2038158	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2092054	0.85[ASN][1000 genomes]
rs2267121	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2267124	0.83[ASN][1000 genomes]
rs3747141	0.87[CHD][hapmap]
rs4140571	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs470100	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs470105	0.91[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5752667	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762393	0.84[ASN][1000 genomes]
rs5762416	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762418	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997319	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6005671	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs720621	0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73425788	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs738451	0.88[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs7625	0.83[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs957601	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs138631	TTC28AS	cis	cerebellum	SCAN
rs138631	ZNF280A	cis	cerebellum	SCAN
rs138631	SEZ6L	cis	cerebellum	SCAN
rs138631	CHEK2	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
3	chr22:28318800-28382000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr22:28319600-28383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr22:28321400-28379000	Weak transcription	Primary B cells from cord blood	blood
6	chr22:28329400-28377800	Weak transcription	Primary T cells from cord blood	blood
7	chr22:28355400-28387800	Weak transcription	Fetal Brain Male	brain
8	chr22:28355600-28378000	Weak transcription	Gastric	stomach
9	chr22:28355800-28378000	Weak transcription	Aorta	Aorta
10	chr22:28355800-28378000	Weak transcription	Left Ventricle	heart
11	chr22:28356600-28378000	Weak transcription	Psoas Muscle	Psoas
12	chr22:28358600-28379400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr22:28359000-28377800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr22:28359200-28377800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr22:28360000-28379400	Weak transcription	Colonic Mucosa	Colon
16	chr22:28360200-28382800	Weak transcription	HSMM	muscle
17	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:28362600-28375800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:28362800-28378000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:28363000-28377800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr22:28363800-28375000	Weak transcription	Lung	lung
22	chr22:28365200-28377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr22:28366200-28378000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr22:28367600-28373800	Weak transcription	Dnd41	blood
25	chr22:28367600-28377800	Weak transcription	Colon Smooth Muscle	Colon
26	chr22:28367800-28377800	Weak transcription	Brain Anterior Caudate	brain
27	chr22:28368200-28373600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr22:28368200-28376000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr22:28368400-28374600	Weak transcription	Adipose Nuclei	Adipose
30	chr22:28368400-28377800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr22:28368400-28383400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr22:28368600-28374400	Weak transcription	Brain Germinal Matrix	brain
33	chr22:28368600-28377600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr22:28368600-28377800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr22:28368800-28373800	Weak transcription	Fetal Muscle Leg	muscle
36	chr22:28368800-28376800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr22:28368800-28377800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr22:28368800-28385800	Weak transcription	Brain Angular Gyrus	brain
39	chr22:28369000-28381200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
41	chr22:28369400-28373800	Weak transcription	Fetal Intestine Large	intestine
42	chr22:28369400-28373800	Weak transcription	Fetal Intestine Small	intestine
43	chr22:28369400-28378000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:28369400-28378000	Weak transcription	Liver	Liver
45	chr22:28369400-28378000	Weak transcription	NHLF	lung
46	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr22:28369800-28377800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr22:28370000-28373800	Weak transcription	Fetal Brain Female	brain
49	chr22:28370200-28376000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr22:28370200-28378000	Weak transcription	Pancreas	Pancrea

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