Variant report

Variant	rs2064148
Chromosome Location	chr1:209909385-209909386
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	chr1:209900061..209902674-chr1:209907942..209909580,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1000282	0.89[EUR][1000 genomes]
rs1000283	0.95[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10157973	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs10863783	0.90[EUR][1000 genomes]
rs10863785	0.90[EUR][1000 genomes]
rs11119327	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11119330	0.90[EUR][1000 genomes]
rs11119331	0.90[EUR][1000 genomes]
rs11119332	0.89[EUR][1000 genomes]
rs11119336	0.89[CEU][hapmap]
rs11119337	0.90[AMR][1000 genomes]
rs11485195	0.90[EUR][1000 genomes]
rs11487866	0.90[EUR][1000 genomes]
rs11487867	0.85[CEU][hapmap]
rs11808690	0.90[EUR][1000 genomes]
rs12034758	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12059226	0.95[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs12060420	0.90[EUR][1000 genomes]
rs12060922	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12086634	0.90[EUR][1000 genomes]
rs12090931	0.90[EUR][1000 genomes]
rs12094117	0.95[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs12116437	0.90[EUR][1000 genomes]
rs12120361	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12129718	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138452	0.90[EUR][1000 genomes]
rs1337531	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1415542	0.95[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs1415544	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17389184	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs17389198	0.90[CEU][hapmap]
rs1999826	0.85[EUR][1000 genomes]
rs2205985	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2236903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272867	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs2282738	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282739	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282741	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884090	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753606	0.80[MKK][hapmap]
rs3765240	0.85[EUR][1000 genomes]
rs3766618	0.85[CEU][hapmap]
rs3766619	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs3817821	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4314885	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4844891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627670	0.90[CEU][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap]
rs6540549	0.95[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6540550	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs6540551	0.80[EUR][1000 genomes]
rs6540553	0.90[CEU][hapmap]
rs6665715	0.90[CEU][hapmap];0.94[TSI][hapmap]
rs6672256	0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs667681	0.90[EUR][1000 genomes]
rs6679099	0.90[EUR][1000 genomes]
rs6679405	0.90[CEU][hapmap]
rs6700223	0.94[AMR][1000 genomes]
rs6702301	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6752	0.90[EUR][1000 genomes]
rs7532324	0.92[EUR][1000 genomes]
rs7539852	0.95[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7548781	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555978	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs909710	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs932335	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs9430012	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs9430014	0.90[EUR][1000 genomes]
rs9430015	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430016	0.95[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs9430017	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv525445	chr1:209885318-209912593	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2064148	SRGAP2	cis	parietal	SCAN
rs2064148	LAMB3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209902400-209915000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:209902400-209915400	Weak transcription	Brain Angular Gyrus	brain
3	chr1:209903000-209915200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:209906400-209914200	Weak transcription	Left Ventricle	heart
5	chr1:209906600-209909400	Weak transcription	Fetal Heart	heart
6	chr1:209906600-209914800	Weak transcription	Right Atrium	heart
7	chr1:209907600-209914800	Weak transcription	Spleen	Spleen
8	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:209907800-209914600	Weak transcription	Right Ventricle	heart
10	chr1:209908000-209909400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:209908000-209909600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:209908000-209909600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:209909000-209909800	Enhancers	Ovary	ovary
14	chr1:209909200-209910600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:209909200-209910800	Enhancers	Liver	Liver

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