Variant report

Variant	rs4845552
Chromosome Location	chr1:153479998-153479999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153478376..153480788-chr1:153481314..153483652,2	K562	blood:
2	chr1:153479765..153482193-chr1:153627799..153629535,2	K562	blood:
3	chr1:153478932..153480622-chr1:153722015..153724458,2	MCF-7	breast:
4	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
5	chr1:153479337..153482179-chr1:153578655..153582224,3	MCF-7	breast:
6	chr1:153341060..153343420-chr1:153479644..153482399,2	MCF-7	breast:
7	chr1:153479500..153482310-chr1:153538620..153542576,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000188643	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs16835366	0.81[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16835368	0.81[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16835382	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16835393	0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17695220	0.91[ASW][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1887039	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1964151	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2339696	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2480695	0.86[GIH][hapmap]
rs28410699	0.93[ASN][1000 genomes]
rs28464843	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28483109	0.86[GIH][hapmap]
rs28632016	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635377	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676601	0.88[ASN][1000 genomes]
rs28707433	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2879553	0.90[JPT][hapmap]
rs3915524	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4017737	0.86[GIH][hapmap]
rs4272569	0.91[ASW][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4430277	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs4845351	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4845352	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4845548	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845549	0.81[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845550	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845551	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845553	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845554	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4845555	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs532652	0.92[GIH][hapmap]
rs550597	0.86[GIH][hapmap];0.85[MEX][hapmap]
rs585215	0.86[GIH][hapmap];0.82[MEX][hapmap]
rs6587743	0.91[ASW][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6587745	0.93[ASN][1000 genomes]
rs6587746	0.93[ASN][1000 genomes]
rs6659755	0.81[ASN][1000 genomes]
rs6660055	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672390	0.81[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs6679509	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6684970	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6690638	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6690712	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6696893	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7515940	0.89[ASN][1000 genomes]
rs7518306	0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7520093	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7534343	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7534347	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7534830	0.89[ASN][1000 genomes]
rs7537898	0.89[ASN][1000 genomes]
rs7544359	0.89[ASN][1000 genomes]
rs9427239	0.92[GIH][hapmap]
rs9436094	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9436095	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hippocampal atrophy	19668339	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4845552	GBA	cis	parietal	SCAN
rs4845552	PSMB4	cis	parietal	SCAN
rs4845552	AQP10	cis	parietal	SCAN
rs4845552	PKLR	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153477800-153480400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:153477800-153480800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:153477800-153480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:153477800-153481000	Enhancers	Fetal Muscle Leg	muscle
5	chr1:153477800-153481200	Enhancers	Ovary	ovary
6	chr1:153478000-153480200	Enhancers	Left Ventricle	heart
7	chr1:153478000-153480400	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:153478000-153481000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:153478000-153481000	Enhancers	Colon Smooth Muscle	Colon
10	chr1:153478000-153481000	Enhancers	HSMM	muscle
11	chr1:153478000-153481200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:153478000-153481200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:153478000-153482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:153478000-153482600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:153478400-153480600	Enhancers	Adipose Nuclei	Adipose
16	chr1:153478400-153480600	Enhancers	Fetal Lung	lung
17	chr1:153478400-153481000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:153478400-153481000	Enhancers	NHLF	lung
19	chr1:153478600-153480600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:153478800-153480000	Enhancers	Right Ventricle	heart
21	chr1:153478800-153480200	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:153478800-153480200	Enhancers	HSMMtube	muscle
23	chr1:153478800-153480400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:153478800-153480600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:153478800-153480800	Enhancers	Fetal Intestine Large	intestine
26	chr1:153478800-153480800	Enhancers	Fetal Stomach	stomach
27	chr1:153478800-153481000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:153478800-153481000	Enhancers	Fetal Intestine Small	intestine
29	chr1:153478800-153481000	Enhancers	NH-A	brain
30	chr1:153478800-153481200	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:153478800-153482200	Enhancers	NHEK	skin
32	chr1:153478800-153482400	Enhancers	HMEC	breast
33	chr1:153479000-153480000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:153479000-153480000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:153479000-153480000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:153479000-153480000	Enhancers	Esophagus	oesophagus
37	chr1:153479000-153480000	Enhancers	Right Atrium	heart
38	chr1:153479000-153480000	Flanking Active TSS	A549	lung
39	chr1:153479000-153480000	Flanking Active TSS	Osteobl	bone
40	chr1:153479000-153480200	Enhancers	Stomach Mucosa	stomach
41	chr1:153479000-153480200	Enhancers	Hela-S3	cervix
42	chr1:153479000-153480800	Enhancers	Colonic Mucosa	Colon
43	chr1:153479000-153481000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:153479200-153480200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr1:153479200-153482000	Weak transcription	Spleen	Spleen
46	chr1:153479200-153485200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:153479200-153487600	Weak transcription	Small Intestine	intestine
48	chr1:153479400-153480200	Flanking Active TSS	HepG2	liver
49	chr1:153479600-153480000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:153479600-153480000	Flanking Active TSS	NHDF-Ad	bronchial

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