Variant report

Variant	rs1982510
Chromosome Location	chr3:47052937-47052938
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47051812-47053140	A549	lung:	n/a	n/a
2	POLR2A	chr3:47051599-47052962	K562	blood:	n/a	n/a
3	POLR2A	chr3:47050917-47053219	K562	blood:	n/a	n/a
4	POLR2A	chr3:47051130-47053407	K562	blood:	n/a	n/a
5	POLR2A	chr3:47050610-47053359	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:47052937-47053362	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:47052806-47052938	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:47050628-47053270	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:47052788-47053155	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:47047465-47053345	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47020574..47023054-chr3:47051075..47053218,2	MCF-7	breast:
2	chr3:47047312..47050228-chr3:47050509..47055807,4	MCF-7	breast:
3	chr11:62607697..62610640-chr3:47050167..47053167,3	K562	blood:
4	chr17:41462096..41467201-chr3:47051647..47053167,7	K562	blood:
5	chr17:41464201..41465744-chr3:47051667..47053167,2	K562	blood:
6	chr3:47051647..47053167-chr3:73159962..73161610,3	K562	blood:
7	chr17:41380516..41382251-chr3:47051647..47053167,2	K562	blood:

No data

Variant related genes	Relation type
NRADDP	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000236383	Chromatin interaction
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17784031	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874265	1.00[ASN][1000 genomes]
rs41290648	1.00[ASN][1000 genomes]
rs4683278	0.83[EUR][1000 genomes]
rs55691981	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786350	0.90[EUR][1000 genomes]
rs56121448	1.00[ASN][1000 genomes]
rs56273245	1.00[ASN][1000 genomes]
rs57249369	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62246361	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246376	0.82[EUR][1000 genomes]
rs62246379	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246402	0.88[EUR][1000 genomes]
rs62246404	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246409	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248895	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62248910	1.00[ASN][1000 genomes]
rs73075647	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079603	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[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	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1982510	PRKAR2A	cis	cerebellum	SCAN
rs1982510	QRICH1	cis	parietal	SCAN
rs1982510	LRRC2	cis	cerebellum	SCAN
rs1982510	MST1R	cis	parietal	SCAN
rs1982510	HYAL2	cis	cerebellum	SCAN
rs1982510	C3orf75	cis	cerebellum	SCAN
rs1982510	IFRD2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47031000-47053000	Strong transcription	Dnd41	blood
2	chr3:47039800-47058000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:47042200-47053000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:47043800-47057800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:47045000-47057600	Weak transcription	HepG2	liver
6	chr3:47048600-47055800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:47049000-47055000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47049000-47055400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:47049800-47058200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:47050200-47058200	Weak transcription	Hela-S3	cervix
11	chr3:47050200-47059000	Weak transcription	A549	lung
12	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
13	chr3:47050400-47057600	Weak transcription	K562	blood
14	chr3:47051200-47058400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:47051400-47055200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:47051400-47056800	Weak transcription	HMEC	breast
17	chr3:47051400-47056800	Weak transcription	NHEK	skin
18	chr3:47051400-47058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:47051400-47064000	Weak transcription	Small Intestine	intestine
20	chr3:47051600-47053600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:47051600-47054200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:47051600-47054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:47051600-47055000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:47051600-47055200	Weak transcription	Liver	Liver
25	chr3:47051600-47055400	Weak transcription	Fetal Kidney	kidney
26	chr3:47051600-47055600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:47051600-47057600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:47051600-47058200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:47051600-47058400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:47051600-47058400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:47051800-47053800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:47051800-47054000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:47051800-47054000	Weak transcription	Thymus	Thymus
34	chr3:47051800-47054200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:47051800-47054200	Weak transcription	Pancreas	Pancrea
36	chr3:47051800-47054400	Weak transcription	Primary B cells from cord blood	blood
37	chr3:47051800-47054400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:47051800-47054800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:47051800-47055200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:47051800-47055200	Enhancers	Fetal Thymus	thymus
41	chr3:47051800-47055400	Weak transcription	Primary T cells from cord blood	blood
42	chr3:47051800-47055600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:47051800-47056800	Weak transcription	Aorta	Aorta
44	chr3:47051800-47056800	Weak transcription	Ovary	ovary
45	chr3:47051800-47057000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:47051800-47060400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:47051800-47061600	Weak transcription	Right Atrium	heart
48	chr3:47051800-47062000	Weak transcription	Psoas Muscle	Psoas
49	chr3:47052000-47053800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:47052000-47053800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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