Variant report

Variant	rs10799590
Chromosome Location	chr1:224822482-224822483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224821183..224823060-chr1:224827666..224830231,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10799277	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10915684	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915694	0.82[CEU][hapmap]
rs10915696	0.95[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs10915698	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs10915699	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12092438	0.90[EUR][1000 genomes]
rs12121558	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs12124262	1.00[CEU][hapmap]
rs12130499	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12132665	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13374487	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1369847	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1436169	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1436171	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1436172	0.95[CEU][hapmap]
rs1465768	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs1603917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1603918	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs169888	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965777	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2050626	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2050627	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2405525	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2648746	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2897161	0.86[EUR][1000 genomes]
rs2936575	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298732	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298733	0.95[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298734	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298735	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs298738	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298739	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2993124	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3012185	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4147293	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4653402	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653404	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653591	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653592	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56881651	0.85[EUR][1000 genomes]
rs61676104	0.84[EUR][1000 genomes]
rs6667034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686604	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6686633	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs67817586	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs713098	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7511897	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7521396	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542995	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs7543218	0.89[EUR][1000 genomes]
rs7544312	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7545574	0.95[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs873594	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10799590	MARK1	cis	cerebellum	SCAN
rs10799590	RAB3GAP2	cis	cerebellum	SCAN
rs10799590	DEGS1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224812800-224825200	Weak transcription	HMEC	breast
2	chr1:224812800-224828200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:224814600-224823000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:224815600-224823200	Enhancers	Fetal Brain Male	brain
5	chr1:224816200-224822600	Enhancers	Fetal Brain Female	brain
6	chr1:224818400-224829400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:224818800-224822600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:224819000-224823400	Enhancers	NHDF-Ad	bronchial
9	chr1:224819400-224824200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:224819800-224822600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:224820000-224824200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:224820200-224823200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:224820400-224840000	Weak transcription	Right Atrium	heart
14	chr1:224820600-224825200	Weak transcription	Fetal Lung	lung
15	chr1:224820800-224822600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:224820800-224822800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:224820800-224822800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:224820800-224823000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:224820800-224823400	Weak transcription	HSMM	muscle
20	chr1:224820800-224824200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:224820800-224824400	Weak transcription	Dnd41	blood
22	chr1:224820800-224825200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:224820800-224827600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:224821000-224822600	Weak transcription	NHLF	lung
25	chr1:224821000-224823800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:224821000-224824800	Weak transcription	HSMMtube	muscle
27	chr1:224821200-224822800	Weak transcription	Pancreas	Pancrea
28	chr1:224821200-224822800	Weak transcription	Osteobl	bone
29	chr1:224821400-224823000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:224821400-224823000	Weak transcription	Ovary	ovary
31	chr1:224821400-224823000	Enhancers	NH-A	brain
32	chr1:224821600-224822600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:224821800-224823200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:224822400-224822600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:224822400-224822600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:224822400-224822600	Enhancers	Gastric	stomach

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