Variant report

Variant	rs2240002
Chromosome Location	chr22:31059250-31059251
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31059169..31061820-chr22:31062802..31064446,3	MCF-7	breast:
2	chr22:31057579..31060597-chr22:31088878..31091753,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167065	Chromatin interaction
ENSG00000184792	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1005887	0.91[CHB][hapmap]
rs1076301	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13054555	0.87[AMR][1000 genomes]
rs1801198	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1981591	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2078976	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267163	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2270013	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3179442	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4513384	0.81[ASN][1000 genomes]
rs4820023	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4820891	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs5749149	0.83[ASN][1000 genomes]
rs5753236	0.86[JPT][hapmap]
rs5753259	0.86[JPT][hapmap]
rs5753265	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5994328	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs5997704	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs5997715	0.81[ASN][1000 genomes]
rs5997731	0.80[AMR][1000 genomes]
rs713853	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757027	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8139950	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2240002	CRYBB2	cis	parietal	SCAN
rs2240002	DUSP18	cis	lymphoblastoid	seeQTL
rs2240002	TCN2	cis	parietal	SCAN
rs2240002	FBXO7	cis	cerebellum	SCAN
rs2240002	RNF185	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31034000-31059400	Weak transcription	Aorta	Aorta
2	chr22:31040200-31060800	Weak transcription	Fetal Brain Male	brain
3	chr22:31045200-31062800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:31045400-31062800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr22:31045400-31062800	Weak transcription	NH-A	brain
6	chr22:31045600-31062800	Weak transcription	HSMMtube	muscle
7	chr22:31045800-31061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr22:31045800-31062200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr22:31046000-31062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:31046000-31062200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr22:31046000-31062600	Weak transcription	HMEC	breast
12	chr22:31046000-31062600	Weak transcription	NHLF	lung
13	chr22:31046800-31062000	Weak transcription	Stomach Mucosa	stomach
14	chr22:31047000-31059400	Weak transcription	Pancreas	Pancrea
15	chr22:31047000-31063000	Weak transcription	Placenta	Placenta
16	chr22:31047000-31063000	Weak transcription	Psoas Muscle	Psoas
17	chr22:31047200-31059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:31050000-31059600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:31051000-31061600	Weak transcription	Small Intestine	intestine
20	chr22:31052400-31059600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:31052400-31060600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:31052800-31061400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr22:31052800-31061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr22:31052800-31062600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:31052800-31062800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr22:31052800-31063000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:31053000-31062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr22:31053400-31062800	Weak transcription	HSMM	muscle
29	chr22:31053600-31059400	Weak transcription	NHEK	skin
30	chr22:31054600-31061200	Strong transcription	Primary T cells from cord blood	blood
31	chr22:31054600-31062000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr22:31054800-31063000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:31055600-31061000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:31055600-31061200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr22:31055800-31060000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr22:31055800-31060800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr22:31056200-31061200	Strong transcription	Fetal Intestine Small	intestine
38	chr22:31056800-31060400	Strong transcription	Lung	lung
39	chr22:31057400-31061400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr22:31057600-31059400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr22:31057600-31060000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr22:31057600-31060000	Strong transcription	Fetal Intestine Large	intestine
43	chr22:31057600-31060000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr22:31057600-31060000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr22:31057600-31060200	Strong transcription	Ovary	ovary
46	chr22:31057600-31060200	Strong transcription	Spleen	Spleen
47	chr22:31057600-31060400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr22:31057600-31060400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:31057600-31060400	Strong transcription	Colonic Mucosa	Colon
50	chr22:31057600-31060400	Strong transcription	Fetal Stomach	stomach

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