Variant report

Variant	rs7534830
Chromosome Location	chr1:153490846-153490847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153489710..153492199-chr1:153643091..153644998,2	MCF-7	breast:
2	chr1:153488456..153491152-chr1:153500196..153502080,2	MCF-7	breast:
3	chr1:153490604..153493387-chr1:153620859..153622534,2	MCF-7	breast:
4	chr1:153480132..153490926-chr1:153537975..153544732,26	MCF-7	breast:
5	chr1:153482414..153491614-chr1:153504332..153509728,11	MCF-7	breast:
6	chr1:153490190..153492255-chr1:153599612..153601121,2	MCF-7	breast:
7	chr1:153490524..153493456-chr1:153634525..153637062,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197956	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000160678	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16835366	0.82[ASN][1000 genomes]
rs16835368	0.82[ASN][1000 genomes]
rs16835382	0.85[ASN][1000 genomes]
rs16835393	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695220	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1887039	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964151	0.85[ASN][1000 genomes]
rs2094217	0.84[EUR][1000 genomes]
rs2094737	0.84[EUR][1000 genomes]
rs2094738	0.86[EUR][1000 genomes]
rs2262587	0.84[EUR][1000 genomes]
rs2339696	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28410699	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28464843	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28632016	0.89[ASN][1000 genomes]
rs28635377	0.89[ASN][1000 genomes]
rs28676601	0.82[ASN][1000 genomes]
rs28707433	0.82[ASN][1000 genomes]
rs3915524	0.85[ASN][1000 genomes]
rs4272569	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4430277	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845351	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845352	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845548	0.82[ASN][1000 genomes]
rs4845549	0.85[ASN][1000 genomes]
rs4845550	0.85[ASN][1000 genomes]
rs4845551	0.85[ASN][1000 genomes]
rs4845552	0.89[ASN][1000 genomes]
rs4845553	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4845554	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845555	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532652	0.84[EUR][1000 genomes]
rs6587743	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587745	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587746	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659755	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6660055	0.82[ASN][1000 genomes]
rs6679509	0.82[ASN][1000 genomes]
rs6684970	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690638	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690712	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696893	0.86[ASN][1000 genomes]
rs7515940	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518306	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520093	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534343	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7534347	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534823	0.83[ASN][1000 genomes]
rs7537898	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544359	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426945	0.84[EUR][1000 genomes]
rs9427239	0.84[EUR][1000 genomes]
rs9427287	0.84[EUR][1000 genomes]
rs9436094	0.82[ASN][1000 genomes]
rs9436095	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv946400	chr1:153488627-153492093	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7534830	RN7SL44P	cis	Nerve Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153481200-153503600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:153483600-153493200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:153483800-153497800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:153488400-153492400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:153488600-153498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:153488800-153492800	Weak transcription	K562	blood
7	chr1:153488800-153497800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:153489000-153491000	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:153489000-153492000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:153489000-153492400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:153489000-153492800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:153489000-153492800	Weak transcription	Colonic Mucosa	Colon
13	chr1:153489000-153493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:153489000-153493200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:153489000-153497800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:153489000-153497800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:153489000-153498000	Weak transcription	Esophagus	oesophagus
18	chr1:153489000-153498000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:153489000-153506000	Weak transcription	Gastric	stomach
20	chr1:153489200-153492000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:153489200-153492000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:153489200-153492800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:153489400-153491000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:153489400-153492800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:153489400-153492800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:153489400-153492800	Weak transcription	Stomach Mucosa	stomach
27	chr1:153489400-153492800	Weak transcription	HMEC	breast
28	chr1:153489400-153493200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:153489400-153493200	Weak transcription	Small Intestine	intestine
30	chr1:153489400-153493400	Weak transcription	NHEK	skin
31	chr1:153489400-153498200	Weak transcription	Hela-S3	cervix
32	chr1:153489600-153492800	Weak transcription	Placenta	Placenta
33	chr1:153490400-153491200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:153490400-153491400	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:153490400-153491400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:153490400-153491800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:153490400-153492000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:153490600-153491200	Enhancers	Fetal Intestine Large	intestine
39	chr1:153490800-153491000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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