Variant report

Variant	rs9284885
Chromosome Location	chr3:48883100-48883101
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr3:48882638-48883142	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48883069-48883119	SAEC	small airway:	n/a
2	chr3:48883069-48883119	RPTEC	kidney:	n/a
3	chr3:48883069-48883119	GM12892	blood:	n/a
4	chr3:48883069-48883119	PrEC	prostate:	n/a
5	chr3:48883069-48883119	SK-N-MC	brain:	n/a
6	chr3:48883069-48883119	NHDF-neo	bronchial:	n/a
7	chr3:48883069-48883119	NHBE	bronchial:	n/a
8	chr3:48883069-48883119	PANC-1	pancreas:	n/a
9	chr3:48883069-48883119	HCT-116	colon:	n/a
10	chr3:48883069-48883119	H1-hESC	embryonic stem cell:	embryo
11	chr3:48883069-48883119	HEK293	kidney:	embryo
12	chr3:48883069-48883119	K562	blood:	n/a
13	chr3:48883069-48883119	HEEpiC	esophagus:	n/a
14	chr3:48883069-48883119	AG09309	skin:	n/a
15	chr3:48883069-48883119	HepG2	liver:	n/a
16	chr3:48883069-48883119	GM06990	blood:	n/a
17	chr3:48883069-48883119	HRE	kidney:	n/a
18	chr3:48883069-48883119	HAEpiC	amniotic membrane:	n/a
19	chr3:48883069-48883119	SK-N-SH_RA	brain:	n/a
20	chr3:48883069-48883119	SK-N-SH	brain:	n/a
21	chr3:48883069-48883119	HRCEpiC	kidney:	n/a
22	chr3:48883069-48883119	AoSMC	blood vessel:	n/a
23	chr3:48883069-48883119	HL-60	blood:	n/a
24	chr3:48883069-48883119	HIPEpiC	eye:	n/a
25	chr3:48883069-48883119	ovcar-3	ovarian:	n/a
26	chr3:48883069-48883119	NH-A	brain:	n/a
27	chr3:48883069-48883119	ECC-1	luminal epithelium:	n/a
28	chr3:48883069-48883119	Caco-2	colon:	n/a
29	chr3:48883069-48883119	A549	lung:	n/a
30	chr3:48883069-48883119	HCF	heart:	n/a
31	chr3:48883069-48883119	HRPEpiC	eye:	n/a
32	chr3:48883069-48883119	U87	brain:	n/a
33	chr3:48883069-48883119	ProgFib	skin:	n/a
34	chr3:48883069-48883119	AG04449	skin:	fetal
35	chr3:48883069-48883119	HMEC	breast:	n/a
36	chr3:48883069-48883119	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:48883069-48883119	HNPCEpiC	eye:	n/a
38	chr3:48883069-48883119	MCF10A-Er-Src	breast:	n/a
39	chr3:48883069-48883119	BJ	skin:	n/a
40	chr3:48883069-48883119	Hepatocyte	liver:	n/a
41	chr3:48883069-48883119	GM12878	blood:	n/a
42	chr3:48883069-48883119	BE2_C	brain:	n/a
43	chr3:48883069-48883119	NT2-D1	testis:	n/a
44	chr3:48883069-48883119	SKMC	muscle:	n/a
45	chr3:48883069-48883119	CMK	blood:	n/a
46	chr3:48883069-48883119	HCPEpiC	choroid plexus:	n/a
47	chr3:48883069-48883119	MCF-7	breast:	n/a
48	chr3:48883069-48883119	Hela-S3	cervix:	n/a
49	chr3:48883069-48883119	Jurkat	blood:	n/a
50	chr3:48883069-48883119	T-47D	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48723157..48725064-chr3:48882807..48884977,2	K562	blood:
2	chr3:48881429..48883622-chr3:49053411..49055620,2	MCF-7	breast:
3	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:
4	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:

No data

Variant related genes	Relation type
PRKAR2A-AS1	TF binding region
PRKAR2A-AS1	CpG island
ENSG00000178149	Chromatin interaction
ENSG00000221883	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000177479	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10780033	0.82[YRI][hapmap]
rs10865953	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs11130176	0.82[YRI][hapmap]
rs1134591	0.82[YRI][hapmap]
rs11707968	0.90[EUR][1000 genomes]
rs12493289	0.82[YRI][hapmap]
rs12632533	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs12715430	0.92[EUR][1000 genomes]
rs13090141	1.00[ASN][1000 genomes]
rs13324192	1.00[ASN][1000 genomes]
rs14018	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs3087866	0.91[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4858800	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs4858830	1.00[CEU][hapmap]
rs4974079	0.81[ASW][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs4974080	0.86[YRI][hapmap]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4974085	0.82[YRI][hapmap]
rs4974087	0.81[ASW][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259536	0.84[EUR][1000 genomes]
rs6442130	0.93[YRI][hapmap]
rs6442131	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446196	0.81[ASW][hapmap];0.86[YRI][hapmap]
rs6446200	0.85[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6446205	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6446252	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs6446253	0.84[YRI][hapmap]
rs6766238	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs6781790	0.82[YRI][hapmap]
rs6787808	1.00[CEU][hapmap]
rs6796790	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs7100	0.91[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs7372883	0.82[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs7429596	0.87[EUR][1000 genomes]
rs7430198	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs7430501	0.82[YRI][hapmap]
rs7431857	0.82[YRI][hapmap]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7621015	0.82[YRI][hapmap]
rs7621226	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7627404	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs7639370	0.91[EUR][1000 genomes]
rs7643368	0.82[YRI][hapmap]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9311430	0.82[YRI][hapmap]
rs9311431	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9311433	0.82[YRI][hapmap]
rs9637481	0.89[YRI][hapmap]
rs9682444	0.81[ASW][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs9755490	0.81[ASW][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs9835307	0.81[ASW][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs9840684	0.82[AFR][1000 genomes]
rs9859473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9860187	0.82[YRI][hapmap]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9873227	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876848	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs9884022	0.81[YRI][hapmap]
rs990211	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs9284885	ZNF589	cis	parietal	SCAN
rs9284885	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9284885	AMT	cis	Whole Blood	GTEx
rs9284885	WDR6	cis	lung	GTEx
rs9284885	AMT	cis	lymphoblastoid	seeQTL
rs9284885	NCKIPSD	cis	parietal	SCAN
rs9284885	WDR6	cis	Muscle Skeletal	GTEx
rs9284885	DALRD3	cis	parietal	SCAN
rs9284885	NICN1	cis	cerebellum	SCAN
rs9284885	AMT	cis	lung	GTEx
rs9284885	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9284885	AMT	cis	Nerve Tibial	GTEx
rs9284885	P4HTM	cis	parietal	SCAN
rs9284885	IQCF1	cis	cerebellum	SCAN
rs9284885	GPX1	cis	parietal	SCAN
rs9284885	NCKIPSD	cis	Nerve Tibial	GTEx
rs9284885	PHF7	cis	parietal	SCAN
rs9284885	WDR6	cis	Heart Left Ventricle	GTEx
rs9284885	AMT	cis	Adipose Subcutaneous	GTEx
rs9284885	NICN1	cis	Thyroid	GTEx
rs9284885	TLR9	cis	parietal	SCAN
rs9284885	AMT	cis	cerebellum	SCAN
rs9284885	AMT	cis	Thyroid	GTEx
rs9284885	LZTFL1	cis	cerebellum	SCAN
rs9284885	AMT	cis	Artery Tibial	GTEx
rs9284885	WDR6	cis	Nerve Tibial	GTEx
rs9284885	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9284885	NICN1	cis	parietal	SCAN
rs9284885	WDR6	cis	parietal	SCAN
rs9284885	QRICH1	cis	cerebellum	SCAN
rs9284885	WDR6	cis	cerebellum	SCAN
rs9284885	DALRD3	cis	cerebellum	SCAN
rs9284885	QRICH1	cis	Nerve Tibial	GTEx
rs9284885	AMT	cis	parietal	SCAN
rs9284885	NICN1-AS1	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48855800-48884000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:48864200-48883200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:48882400-48883600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:48882400-48883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:48882400-48884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:48882400-48884000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:48882400-48884000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:48882400-48884200	Enhancers	Liver	Liver
9	chr3:48882600-48883200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr3:48882600-48883200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:48882600-48883200	Enhancers	Duodenum Mucosa	Duodenum
12	chr3:48882600-48883200	Enhancers	Fetal Intestine Small	intestine
13	chr3:48882600-48883400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:48882600-48883400	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
15	chr3:48882600-48883600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:48882600-48883600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr3:48882600-48883600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:48882600-48883600	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr3:48882600-48883600	Flanking Active TSS	Hela-S3	cervix
20	chr3:48882600-48883800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:48882600-48884000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:48882600-48884000	Enhancers	Primary T cells from cord blood	blood
23	chr3:48882600-48884000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr3:48882600-48884000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:48882600-48884000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:48882600-48884000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48882600-48884000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:48882600-48884000	Enhancers	Fetal Lung	lung
29	chr3:48882600-48884000	Enhancers	Fetal Stomach	stomach
30	chr3:48882600-48884000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr3:48882600-48884200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:48882600-48884200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:48882600-48884200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:48882600-48884200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:48882600-48884200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:48882600-48884200	Enhancers	Brain Germinal Matrix	brain
37	chr3:48882600-48884200	Enhancers	Brain Substantia Nigra	brain
38	chr3:48882600-48884200	Enhancers	Fetal Intestine Large	intestine
39	chr3:48882600-48884200	Enhancers	Stomach Mucosa	stomach
40	chr3:48882600-48884400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr3:48882600-48884400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:48882600-48884400	Enhancers	Small Intestine	intestine
43	chr3:48882600-48885600	Active TSS	GM12878-XiMat	blood
44	chr3:48882600-48886000	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:48882800-48883200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:48882800-48883200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr3:48882800-48883200	Flanking Active TSS	Ovary	ovary
48	chr3:48882800-48883200	Enhancers	Spleen	Spleen
49	chr3:48882800-48883200	Enhancers	HepG2	liver
50	chr3:48882800-48883200	Enhancers	NHEK	skin

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