Variant report

Variant	rs4140571
Chromosome Location	chr22:28423378-28423379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28421365..28425106-chr22:28428246..28431609,4	MCF-7	breast:
2	chr22:28422055..28424855-chr22:28425948..28427565,2	K562	blood:
3	chr22:28421666..28423671-chr22:28428407..28430041,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028364	0.81[JPT][hapmap]
rs118839	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12171034	0.91[ASN][1000 genomes]
rs138631	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs138638	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs138650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs138675	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs138683	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs138685	0.82[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548235	0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2038158	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2092054	0.91[ASN][1000 genomes]
rs2267121	0.86[TSI][hapmap]
rs3747141	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs470100	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs470105	0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752667	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762416	0.83[EUR][1000 genomes]
rs5762418	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6005671	0.89[CEU][hapmap];0.88[CHD][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs720621	0.85[CHD][hapmap];0.84[TSI][hapmap]
rs73425788	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs738451	0.82[CHD][hapmap];0.86[TSI][hapmap]
rs7625	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs957601	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	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
rs4140571	CHEK2	cis	cerebellum	SCAN
rs4140571	SEZ6L	cis	cerebellum	SCAN
rs4140571	ZNF280A	cis	cerebellum	SCAN
rs4140571	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28399400-28425800	Weak transcription	Liver	Liver
2	chr22:28409000-28428000	Genic enhancers	Fetal Muscle Leg	muscle
3	chr22:28409400-28430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:28410200-28423400	Weak transcription	Gastric	stomach
5	chr22:28410400-28424200	Weak transcription	Aorta	Aorta
6	chr22:28411000-28423600	Weak transcription	Fetal Intestine Large	intestine
7	chr22:28416000-28425000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr22:28416600-28431000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr22:28416800-28423400	Weak transcription	Pancreas	Pancrea
10	chr22:28416800-28424200	Strong transcription	Fetal Intestine Small	intestine
11	chr22:28416800-28425200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:28417000-28423400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr22:28417000-28425800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:28417200-28424600	Weak transcription	Colonic Mucosa	Colon
15	chr22:28417200-28426000	Weak transcription	Brain Angular Gyrus	brain
16	chr22:28417400-28423800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:28417400-28424200	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:28417400-28424800	Weak transcription	NHLF	lung
19	chr22:28417600-28424600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr22:28417600-28425400	Weak transcription	NHDF-Ad	bronchial
21	chr22:28417800-28423600	Weak transcription	Fetal Lung	lung
22	chr22:28417800-28426200	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr22:28418400-28424400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:28418600-28424200	Weak transcription	Placenta	Placenta
25	chr22:28418600-28429800	Strong transcription	Dnd41	blood
26	chr22:28419600-28426000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr22:28419800-28427400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr22:28420000-28423400	Weak transcription	Fetal Thymus	thymus
29	chr22:28420200-28426400	Enhancers	Psoas Muscle	Psoas
30	chr22:28420400-28425000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:28420400-28425600	Enhancers	Right Ventricle	heart
32	chr22:28421000-28423800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:28421200-28424800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr22:28421200-28425600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:28421600-28424800	Weak transcription	HSMM	muscle
36	chr22:28421600-28425000	Weak transcription	HSMMtube	muscle
37	chr22:28421600-28427200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:28421800-28425800	Enhancers	Spleen	Spleen
39	chr22:28421800-28427000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr22:28422000-28425000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr22:28422000-28426400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr22:28422200-28423400	Weak transcription	Ovary	ovary
43	chr22:28422200-28425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:28422200-28426800	Enhancers	Primary hematopoietic stem cells	blood
45	chr22:28422400-28423400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr22:28422400-28426800	Strong transcription	Primary T cells from cord blood	blood
47	chr22:28422600-28426000	Enhancers	Fetal Heart	heart
48	chr22:28422800-28424800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr22:28422800-28426400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:28423000-28423800	Enhancers	Adipose Nuclei	Adipose

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