Variant report

Variant	rs2498982
Chromosome Location	chr1:62516683-62516684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12066543	0.82[ASN][1000 genomes]
rs12097259	0.86[ASN][1000 genomes]
rs12098048	0.88[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12732781	0.90[ASN][1000 genomes]
rs12750860	0.86[ASN][1000 genomes]
rs1332633	0.88[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13374203	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1412621	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17122997	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2183996	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2365741	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2476181	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476185	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2476188	0.81[GIH][hapmap]
rs2498981	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072368	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072369	0.86[ASN][1000 genomes]
rs4072372	0.86[ASN][1000 genomes]
rs4073681	0.86[ASN][1000 genomes]
rs4316389	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915602	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6689358	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699078	0.83[GIH][hapmap]
rs7515090	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7517333	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7520924	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7526522	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7537239	0.83[EUR][1000 genomes]
rs7551942	0.87[ASN][1000 genomes]
rs991191	0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[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	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2498982	AK4	cis	cerebellum	SCAN
rs2498982	INADL	cis	cerebellum	SCAN
rs2498982	RAVER2	cis	cerebellum	SCAN
rs2498982	NFIA	cis	cerebellum	SCAN
rs2498982	L1TD1	cis	cerebellum	SCAN
rs2498982	DAB1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:62488400-62521200	Weak transcription	Ovary	ovary
12	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
14	chr1:62495200-62544800	Weak transcription	Liver	Liver
15	chr1:62502200-62520600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:62503600-62520200	Weak transcription	Fetal Brain Male	brain
17	chr1:62504800-62531400	Weak transcription	Aorta	Aorta
18	chr1:62507200-62523000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:62507200-62523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:62507400-62524600	Weak transcription	HepG2	liver
21	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
22	chr1:62508800-62532000	Weak transcription	Fetal Stomach	stomach
23	chr1:62511400-62531600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:62511400-62531800	Weak transcription	NHEK	skin
25	chr1:62511600-62518800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:62511600-62520000	Weak transcription	Right Ventricle	heart
27	chr1:62511600-62522600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:62511600-62522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:62511600-62531200	Weak transcription	Lung	lung
30	chr1:62511800-62517600	Weak transcription	Fetal Intestine Small	intestine
31	chr1:62511800-62521600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:62511800-62522600	Weak transcription	Psoas Muscle	Psoas
33	chr1:62511800-62523200	Weak transcription	Fetal Heart	heart
34	chr1:62511800-62529600	Weak transcription	Right Atrium	heart
35	chr1:62512200-62524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:62512400-62518800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:62513600-62518800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:62514000-62522800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:62514000-62522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:62514000-62522800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:62514000-62524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:62515200-62516800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:62515200-62523200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:62515400-62519000	Strong transcription	Fetal Intestine Large	intestine
45	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:62515800-62522600	Weak transcription	Left Ventricle	heart
47	chr1:62516000-62517400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:62516000-62517600	Strong transcription	HMEC	breast
49	chr1:62516000-62518200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:62516000-62518800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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