Variant report

Variant	rs7520924
Chromosome Location	chr1:62500555-62500556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10127708	0.89[ASN][1000 genomes]
rs10127709	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs12098048	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1332630	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs1332633	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13374203	0.88[CEU][hapmap];0.80[CHB][hapmap];0.81[YRI][hapmap]
rs1412621	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2183996	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2365741	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2476181	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2476185	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2498981	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2498982	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]
rs3924471	0.85[CHB][hapmap]
rs4072368	0.88[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4316389	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4915602	0.88[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6689358	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7515090	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7517333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526522	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7537239	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7537323	0.84[CHD][hapmap]

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	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	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7520924	OMA1	cis	parietal	SCAN
rs7520924	AK4	cis	cerebellum	SCAN
rs7520924	NFIA	cis	cerebellum	SCAN
rs7520924	DAB1	cis	parietal	SCAN
rs7520924	INADL	cis	cerebellum	SCAN

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

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	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62459200-62511200	Weak transcription	Gastric	stomach
6	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:62460200-62516000	Weak transcription	HMEC	breast
10	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:62484600-62506000	Weak transcription	NHEK	skin
16	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:62488400-62521200	Weak transcription	Ovary	ovary
19	chr1:62491800-62511200	Weak transcription	Psoas Muscle	Psoas
20	chr1:62494600-62504600	Weak transcription	Aorta	Aorta
21	chr1:62494600-62511200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
24	chr1:62494800-62505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:62495000-62504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:62495000-62515200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:62495200-62516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:62495200-62544800	Weak transcription	Liver	Liver
29	chr1:62496200-62504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:62497200-62515000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:62498600-62500600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:62499400-62500800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:62499400-62501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:62499400-62504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:62499600-62501600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:62499600-62502000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:62499600-62505400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:62499800-62501400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:62500000-62503000	Weak transcription	Left Ventricle	heart
40	chr1:62500000-62504400	Weak transcription	Right Atrium	heart
41	chr1:62500000-62504600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:62500000-62505200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:62500000-62505400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:62500000-62506400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:62500000-62515400	Weak transcription	Fetal Intestine Large	intestine
46	chr1:62500200-62500600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:62500400-62500600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:62500400-62505400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:62500400-62505400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:62500400-62511200	Weak transcription	Right Ventricle	heart

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