Variant report

Variant	rs1520666
Chromosome Location	chr3:157989083-157989084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157989031..157991493-chr3:157993072..157995129,2	K562	blood:
2	chr3:157988669..157990531-chr3:157993629..157996480,3	K562	blood:
3	chr3:157987978..157990899-chr3:157994942..157996783,2	MCF-7	breast:
4	chr3:157918972..157921649-chr3:157988884..157990990,2	K562	blood:

Variant related genes	Relation type
ENSG00000174891	Chromatin interaction
ENSG00000241723	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1095625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095631	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095632	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103981	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915781	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193519	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520657	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589522	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608099	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656360	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714517	0.93[EUR][1000 genomes]
rs1724650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724725	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1730038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680416	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441191	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779266	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788695	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804180	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs698978	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170371	0.87[EUR][1000 genomes]
rs7651712	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827103	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827105	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827107	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827115	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827116	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827117	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827119	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827133	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827152	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827182	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827183	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827189	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845600	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520666	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157963800-157995800	Weak transcription	Gastric	stomach
2	chr3:157984800-158001200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:157985000-157993800	Weak transcription	Ovary	ovary
4	chr3:157985200-157997200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:157985200-157997200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:157985600-157998400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:157986000-157998000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:157986200-157989800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:157986200-157992400	Weak transcription	Dnd41	blood
10	chr3:157986200-157993000	Weak transcription	Primary T cells from cord blood	blood
11	chr3:157986200-157997200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:157986200-158001200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:157986200-158006600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:157986400-157991400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:157986400-157992200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:157986400-157992400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:157986400-157997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:157986400-157997200	Weak transcription	Fetal Lung	lung
19	chr3:157986400-157997800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:157986400-157999200	Weak transcription	Adipose Nuclei	Adipose
21	chr3:157986400-158040000	Weak transcription	Primary B cells from cord blood	blood
22	chr3:157987600-157996000	Weak transcription	K562	blood
23	chr3:157988200-157989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:157988200-157989600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:157988200-157989600	Weak transcription	Fetal Brain Female	brain
26	chr3:157988200-157990000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:157988200-157992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:157988200-157993800	Weak transcription	Aorta	Aorta
29	chr3:157988200-157993800	Weak transcription	Left Ventricle	heart
30	chr3:157988200-157994000	Weak transcription	Lung	lung
31	chr3:157988200-157999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:157988200-158009600	Weak transcription	Pancreas	Pancrea
33	chr3:157988400-157990000	Weak transcription	NHEK	skin
34	chr3:157988400-157995600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:157988400-157997600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:157988400-158001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:157988600-157992400	Weak transcription	GM12878-XiMat	blood
38	chr3:157989000-157989800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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