Variant report

Variant	rs1532163
Chromosome Location	chr5:52856716-52856717
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	chr19:49466894..49467622-chr5:52856230..52856915,2	NB4	blood:
2	chr2:11680129..11682138-chr5:52854884..52857698,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267898	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10063311	0.83[AMR][1000 genomes]
rs10072971	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10077935	0.87[ASN][1000 genomes]
rs1030228	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12521381	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1465445	1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1552649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173905	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1844698	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187659	0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198941	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs2130744	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256083	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256085	0.83[ASN][1000 genomes]
rs256087	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256090	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256097	0.83[CHD][hapmap]
rs256107	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256110	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256112	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256113	0.87[ASN][1000 genomes]
rs256116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256117	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607501	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607502	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2607511	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636991	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2637004	0.83[ASN][1000 genomes]
rs2637027	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2637030	0.86[CHD][hapmap]
rs271217	0.84[ASN][1000 genomes]
rs31302	0.86[CHD][hapmap];0.81[GIH][hapmap]
rs31303	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs370594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs372006	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs372135	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs375956	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376566	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs381374	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs399141	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs403207	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147740	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs423014	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs423872	0.86[CHD][hapmap];0.81[GIH][hapmap]
rs424955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs429384	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs430427	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs435187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439552	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439641	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs449160	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs549131	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6881928	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7728496	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7731940	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786335	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889291	0.89[JPT][hapmap]
rs889292	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs923609	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1532163	NDUFS4	cis	parietal	SCAN
rs1532163	GPBP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52855600-52858200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:52855800-52856800	Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr5:52855800-52857000	Active TSS	Primary T cells from cord blood	blood
4	chr5:52855800-52857200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:52855800-52857200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:52855800-52857200	Active TSS	Hela-S3	cervix
7	chr5:52855800-52857400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:52855800-52857400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:52855800-52857400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr5:52855800-52857400	Active TSS	Brain Anterior Caudate	brain
11	chr5:52855800-52857400	Active TSS	Brain Cingulate Gyrus	brain
12	chr5:52855800-52857400	Active TSS	Brain Hippocampus Middle	brain
13	chr5:52855800-52857400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:52855800-52857400	Active TSS	Colon Smooth Muscle	Colon
15	chr5:52855800-52857400	Active TSS	Fetal Brain Female	brain
16	chr5:52855800-52857400	Active TSS	Fetal Lung	lung
17	chr5:52855800-52857400	Active TSS	A549	lung
18	chr5:52855800-52857600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:52855800-52857600	Active TSS	HMEC	breast
20	chr5:52855800-52857600	Active TSS	K562	blood
21	chr5:52855800-52857800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:52855800-52857800	Active TSS	Right Atrium	heart
23	chr5:52855800-52857800	Active TSS	Stomach Smooth Muscle	stomach
24	chr5:52855800-52858000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:52855800-52858200	Active TSS	NHLF	lung
26	chr5:52856000-52856800	Active TSS	Primary B cells from cord blood	blood
27	chr5:52856000-52856800	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr5:52856000-52856800	Active TSS	Liver	Liver
29	chr5:52856000-52857000	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr5:52856000-52857000	Active TSS	Brain Substantia Nigra	brain
31	chr5:52856000-52857000	Active TSS	Duodenum Mucosa	Duodenum
32	chr5:52856000-52857000	Active TSS	Fetal Kidney	kidney
33	chr5:52856000-52857000	Active TSS	Osteobl	bone
34	chr5:52856000-52857200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr5:52856000-52857200	Active TSS	Colonic Mucosa	Colon
36	chr5:52856000-52857200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52856000-52857200	Active TSS	Placenta	Placenta
38	chr5:52856000-52857200	Active TSS	Rectal Smooth Muscle	rectum
39	chr5:52856000-52857200	Bivalent/Poised TSS	HepG2	liver
40	chr5:52856000-52857400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr5:52856000-52857400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:52856000-52857400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:52856000-52857400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:52856000-52857400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:52856000-52857400	Active TSS	Fetal Heart	heart
46	chr5:52856000-52857400	Active TSS	Fetal Intestine Large	intestine
47	chr5:52856000-52857400	Active TSS	Fetal Muscle Trunk	muscle
48	chr5:52856000-52857400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr5:52856000-52857400	Active TSS	Thymus	Thymus
50	chr5:52856000-52857600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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