Variant report

Variant	rs4705559
Chromosome Location	chr5:112050122-112050123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112042876..112045177-chr5:112046298..112050901,7	K562	blood:
2	chr5:112048029..112050157-chr5:112062177..112064729,3	K562	blood:
3	chr5:112040661..112045747-chr5:112046493..112054139,9	MCF-7	breast:
4	chr5:112048029..112050157-chr5:112062622..112064729,2	K562	blood:
5	chr5:112043010..112045071-chr5:112047390..112050784,5	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10051624	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10071425	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10072068	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073398	0.81[EUR][1000 genomes]
rs10075281	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10075323	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10075377	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10076641	0.85[EUR][1000 genomes]
rs10213844	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10463642	0.87[ASN][1000 genomes]
rs10477483	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241182	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241183	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11241184	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241185	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11749632	0.81[EUR][1000 genomes]
rs11749701	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11954856	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12332692	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12513787	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12513804	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12518091	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12658609	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12659119	0.81[EUR][1000 genomes]
rs13156251	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13173990	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1441367	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1465910	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1530256	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153544	0.82[CEU][hapmap]
rs17134858	0.84[CHB][hapmap]
rs17285505	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1816769	0.85[CEU][hapmap]
rs1866924	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1914	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1968557	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1974786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2019720	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2020383	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2099810	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229992	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2251913	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2253987	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2289484	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2431239	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2431241	0.91[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2431512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2439589	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2439595	0.89[CHB][hapmap]
rs2464803	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes]
rs2545156	0.84[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs2545158	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2546106	0.83[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs2546107	0.82[AFR][1000 genomes]
rs2546108	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2546110	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2546112	0.84[CHB][hapmap]
rs2546117	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707763	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2707765	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs28373740	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28578275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2901844	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909786	0.85[CEU][hapmap]
rs2909787	0.85[CEU][hapmap]
rs2909958	0.89[CEU][hapmap]
rs3317	0.92[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs351768	0.85[CEU][hapmap]
rs351772	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35414976	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs368575	0.84[CEU][hapmap]
rs374613	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs382427	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs3846716	0.85[TSI][hapmap]
rs390092	0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs395858	0.84[CEU][hapmap]
rs396321	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs4099181	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs414098	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs419155	0.92[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs448162	0.92[ASW][hapmap];0.85[CHD][hapmap]
rs454886	0.84[CHB][hapmap]
rs458906	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs460137	0.84[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs467033	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs469886	0.85[CEU][hapmap]
rs4705486	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705573	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705624	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs511906	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs548710	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs566419	0.87[CEU][hapmap]
rs62364017	0.82[EUR][1000 genomes]
rs6594646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6862050	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6864688	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs6867243	0.82[EUR][1000 genomes]
rs6879057	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6894351	0.85[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6898133	0.81[EUR][1000 genomes]
rs7704618	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727738	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818428	0.85[CEU][hapmap]
rs818797	0.85[CEU][hapmap]
rs861674	0.85[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs9326862	0.85[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs9326863	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs953916	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647582	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9647583	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4705559	NCRNA00219	cis	parietal	SCAN
rs4705559	REEP5	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112044800-112050200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:112044800-112052200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:112044800-112058000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:112044800-112058800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:112045200-112053200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:112045200-112054000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:112045400-112050800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112045400-112051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:112045400-112052600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:112045400-112053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:112045400-112054400	Weak transcription	NHEK	skin
12	chr5:112045400-112062000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:112045600-112054000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:112045600-112054600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:112045600-112060200	Weak transcription	NHLF	lung
16	chr5:112045600-112061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:112045600-112063600	Weak transcription	Ovary	ovary
18	chr5:112045800-112054000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:112046000-112050600	Weak transcription	Fetal Kidney	kidney
20	chr5:112046000-112054000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:112046200-112050200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:112046400-112051800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:112046400-112053200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:112046800-112050400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:112046800-112053200	Weak transcription	Fetal Lung	lung
27	chr5:112047000-112060400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr5:112047000-112061600	Weak transcription	Aorta	Aorta
29	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:112047200-112052400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:112047200-112054000	Weak transcription	Right Ventricle	heart
32	chr5:112047400-112052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:112047400-112053200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:112047400-112054000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:112047400-112056200	Weak transcription	Dnd41	blood
36	chr5:112047400-112058600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:112047400-112060400	Weak transcription	Fetal Intestine Large	intestine
38	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
39	chr5:112047600-112050200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:112047600-112054000	Weak transcription	Pancreas	Pancrea
41	chr5:112047600-112061600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:112048200-112052200	Weak transcription	Primary T cells from cord blood	blood
43	chr5:112048200-112054000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:112048200-112054000	Weak transcription	Gastric	stomach
45	chr5:112048200-112058200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:112048400-112053800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:112048400-112061200	Weak transcription	Fetal Intestine Small	intestine
48	chr5:112048800-112050200	Enhancers	Brain Germinal Matrix	brain
49	chr5:112049000-112050200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr5:112049200-112050400	Weak transcription	Brain Anterior Caudate	brain

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