Variant report

Variant	rs5753540
Chromosome Location	chr22:31681649-31681650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31681629..31683891-chr22:31739597..31743565,3	MCF-7	breast:
2	chr22:31680141..31683839-chr22:31741911..31744786,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10483159	1.00[EUR][1000 genomes]
rs11089493	0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11089501	1.00[EUR][1000 genomes]
rs11089502	1.00[EUR][1000 genomes]
rs11089503	1.00[EUR][1000 genomes]
rs11089504	1.00[EUR][1000 genomes]
rs12165685	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12168242	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12484282	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12484775	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12484966	1.00[EUR][1000 genomes]
rs12485176	1.00[EUR][1000 genomes]
rs12485177	1.00[EUR][1000 genomes]
rs17220418	0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17820958	0.84[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17821132	1.00[EUR][1000 genomes]
rs1859677	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1968024	1.00[EUR][1000 genomes]
rs2057951	0.84[JPT][hapmap]
rs2073856	0.84[CHB][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073859	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073860	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073861	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074734	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2158779	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240424	0.84[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240427	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2267168	0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273248	1.00[EUR][1000 genomes]
rs2283882	0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28678535	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28872513	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899161	0.89[JPT][hapmap]
rs3747153	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3747154	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3747155	1.00[EUR][1000 genomes]
rs3788434	1.00[EUR][1000 genomes]
rs4293639	0.88[ASN][1000 genomes]
rs5749222	0.86[JPT][hapmap]
rs5749225	0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs5749230	0.92[ASN][1000 genomes]
rs5749233	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749235	0.92[ASN][1000 genomes]
rs5749236	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749239	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749240	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749241	0.96[ASN][1000 genomes]
rs5749247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749252	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749255	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749257	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5749258	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749262	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749263	1.00[EUR][1000 genomes]
rs5753485	0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs5753494	0.89[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5753502	0.85[ASN][1000 genomes]
rs5753506	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753509	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753511	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753512	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753513	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753516	0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753519	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753523	0.91[ASN][1000 genomes]
rs5753525	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753526	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753527	0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753529	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753532	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753534	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753535	0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753542	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5753554	0.89[ASN][1000 genomes]
rs5753555	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753556	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753561	0.94[ASN][1000 genomes]
rs5753566	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753569	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753571	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753572	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753574	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs57775002	0.81[ASN][1000 genomes]
rs58856347	1.00[EUR][1000 genomes]
rs59416609	1.00[EUR][1000 genomes]
rs5994386	0.88[ASN][1000 genomes]
rs5997921	0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs5997959	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs713619	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7286926	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7292620	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73396257	1.00[EUR][1000 genomes]
rs874356	0.81[JPT][hapmap]
rs9619178	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9621212	0.89[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9621215	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9621220	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9621226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9621236	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9621247	1.00[EUR][1000 genomes]
rs9621252	1.00[EUR][1000 genomes]
rs9621261	1.00[EUR][1000 genomes]
rs9621264	1.00[EUR][1000 genomes]
rs9621265	1.00[EUR][1000 genomes]
rs9621270	1.00[EUR][1000 genomes]
rs9680708	0.83[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	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
2	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
3	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
5	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
6	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
9	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
12	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
14	chr22:31673000-31681800	Strong transcription	Placenta	Placenta
15	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
19	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
20	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
21	chr22:31674600-31682600	Strong transcription	Rectal Smooth Muscle	rectum
22	chr22:31675400-31682200	Strong transcription	Colon Smooth Muscle	Colon
23	chr22:31675400-31686400	Weak transcription	NH-A	brain
24	chr22:31675800-31685000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr22:31676200-31682200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr22:31676400-31684600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr22:31676800-31682200	Weak transcription	GM12878-XiMat	blood
28	chr22:31676800-31682200	Weak transcription	HSMMtube	muscle
29	chr22:31676800-31684800	Weak transcription	Hela-S3	cervix
30	chr22:31676800-31685000	Weak transcription	Osteobl	bone
31	chr22:31677000-31684600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:31678000-31686400	Weak transcription	HMEC	breast
33	chr22:31678200-31684000	Strong transcription	Left Ventricle	heart
34	chr22:31678800-31682600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr22:31679000-31685400	Weak transcription	Liver	Liver
36	chr22:31679200-31682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr22:31679200-31685000	Weak transcription	Fetal Lung	lung
38	chr22:31679200-31685800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr22:31679200-31686400	Weak transcription	HSMM	muscle
40	chr22:31679200-31686600	Weak transcription	Ovary	ovary
41	chr22:31679400-31682200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr22:31679400-31684800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr22:31679400-31685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr22:31679400-31685800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr22:31679400-31686400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr22:31679600-31684000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:31680000-31685200	Genic enhancers	Fetal Thymus	thymus
48	chr22:31680000-31685200	Weak transcription	NHEK	skin
49	chr22:31680200-31684400	Enhancers	Primary hematopoietic stem cells	blood
50	chr22:31680200-31685400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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