Variant report

Variant	rs7514452
Chromosome Location	chr1:154438084-154438085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154425985..154428453-chr1:154436104..154438755,2	MCF-7	breast:
2	chr1:154401668..154404538-chr1:154437073..154438684,2	K562	blood:
3	chr1:154427927..154430760-chr1:154437313..154439105,2	K562	blood:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10047079	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10752641	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10908839	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11490956	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12403537	0.89[EUR][1000 genomes]
rs12405637	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12406822	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12408461	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2229238	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35699331	0.95[ASN][1000 genomes]
rs3811448	0.80[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3811449	0.88[EUR][1000 genomes]
rs4072391	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41269915	0.86[EUR][1000 genomes]
rs41308419	0.86[EUR][1000 genomes]
rs41313910	0.88[EUR][1000 genomes]
rs4240872	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs4341355	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4379670	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390168	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs4509570	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4633282	0.86[EUR][1000 genomes]
rs4639752	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs4845625	0.83[ASW][hapmap]
rs55668699	0.87[ASN][1000 genomes]
rs57783436	0.88[EUR][1000 genomes]
rs58348886	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58710275	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58881140	0.88[EUR][1000 genomes]
rs59084843	0.88[EUR][1000 genomes]
rs59239860	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59741504	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59838898	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60092776	0.87[EUR][1000 genomes]
rs60255122	0.85[EUR][1000 genomes]
rs60368585	0.86[EUR][1000 genomes]
rs60498985	0.87[EUR][1000 genomes]
rs60760897	0.86[EUR][1000 genomes]
rs60931472	0.88[EUR][1000 genomes]
rs61275241	0.86[EUR][1000 genomes]
rs61403567	0.86[EUR][1000 genomes]
rs61559765	0.88[EUR][1000 genomes]
rs61698846	0.86[EUR][1000 genomes]
rs6427672	0.90[ASN][1000 genomes]
rs6669229	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672087	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs6674171	0.85[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6681207	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs6687597	0.95[ASN][1000 genomes]
rs6689393	0.83[ASW][hapmap]
rs6698040	0.95[ASN][1000 genomes]
rs72999415	0.88[EUR][1000 genomes]
rs72999419	0.87[EUR][1000 genomes]
rs72999422	0.88[EUR][1000 genomes]
rs73018293	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73020232	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73020234	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73020246	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73023331	0.86[EUR][1000 genomes]
rs73023339	0.86[EUR][1000 genomes]
rs73023346	0.88[EUR][1000 genomes]
rs73023348	0.88[EUR][1000 genomes]
rs73023349	0.88[EUR][1000 genomes]
rs7526293	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537291	0.95[ASN][1000 genomes]
rs7537316	0.95[ASN][1000 genomes]
rs7546068	0.95[ASN][1000 genomes]
rs7546552	0.95[ASN][1000 genomes]
rs7546555	0.95[ASN][1000 genomes]
rs7551873	0.80[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7556449	0.80[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7514452	PMF1	cis	cerebellum	SCAN
rs7514452	TDRD10	cis	lung	GTEx
rs7514452	LCE3C	cis	cerebellum	SCAN
rs7514452	PI4KB	cis	parietal	SCAN
rs7514452	CDC42SE1	cis	cerebellum	SCAN
rs7514452	UBAP2L	cis	parietal	SCAN
rs7514452	PMF1	cis	parietal	SCAN
rs7514452	CDC42SE1	cis	parietal	SCAN
rs7514452	ADAMTSL4	cis	parietal	SCAN
rs7514452	LCE3A	cis	parietal	SCAN
rs7514452	ARNT	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:154426800-154442200	Weak transcription	HepG2	liver
5	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:154427800-154464800	Weak transcription	Ovary	ovary
7	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:154430400-154438800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:154434400-154438600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:154434800-154439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
16	chr1:154435800-154438200	Enhancers	HSMMtube	muscle
17	chr1:154436000-154438600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:154436000-154439000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154436200-154438200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:154436200-154440800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:154436200-154441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:154436200-154441200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:154436400-154438200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:154436400-154438200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:154436400-154438400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:154436400-154438600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:154436400-154441800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:154436400-154446400	Weak transcription	NHEK	skin
29	chr1:154436400-154446600	Weak transcription	HMEC	breast
30	chr1:154436600-154438400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:154436600-154438400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:154436600-154438400	Weak transcription	Right Atrium	heart
33	chr1:154436600-154438600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:154436600-154438600	Weak transcription	K562	blood
35	chr1:154436600-154438800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:154436600-154439400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:154436600-154440600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:154436600-154441000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:154436600-154441200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:154436600-154441200	Weak transcription	Fetal Brain Male	brain
41	chr1:154436600-154441600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:154436600-154441600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:154436600-154446800	Weak transcription	NHDF-Ad	bronchial
44	chr1:154436600-154450600	Weak transcription	HUVEC	blood vessel
45	chr1:154437200-154438600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:154437200-154439200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:154437200-154439400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:154437200-154441600	Strong transcription	Lung	lung
49	chr1:154437400-154438200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:154437400-154438400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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