Variant report

Variant	rs3859015
Chromosome Location	chr15:73626970-73626971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1017808	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10518997	1.00[YRI][hapmap]
rs11072407	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11072408	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11072411	0.89[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072412	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072415	0.96[ASN][1000 genomes]
rs1119251	0.82[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11634045	0.89[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11636981	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12439852	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12440576	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442755	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591304	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594776	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12901272	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1382782	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1564347	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16957683	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1878940	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2061890	0.86[AFR][1000 genomes]
rs2252725	0.80[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs2292915	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415145	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2415146	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2660821	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2660824	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2680340	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2680341	0.80[AMR][1000 genomes]
rs34456824	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34953385	0.83[AFR][1000 genomes]
rs35348961	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35391014	0.82[AMR][1000 genomes]
rs35608416	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35778649	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36072085	0.86[AFR][1000 genomes]
rs3743496	1.00[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784795	0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3826043	0.84[ASN][1000 genomes]
rs3859014	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472681	0.85[ASN][1000 genomes]
rs476846	0.96[ASN][1000 genomes]
rs4776631	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4777592	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs486267	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs488156	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs489531	0.80[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap]
rs491742	0.94[ASN][1000 genomes]
rs492362	0.86[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs498005	0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs498868	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs519946	0.96[ASN][1000 genomes]
rs519970	0.96[ASN][1000 genomes]
rs559260	0.80[AMR][1000 genomes]
rs563076	0.80[AMR][1000 genomes]
rs564765	0.80[AMR][1000 genomes]
rs568435	0.95[ASN][1000 genomes]
rs569532	0.96[ASN][1000 genomes]
rs570001	0.86[ASN][1000 genomes]
rs573397	0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs576813	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs59628124	0.86[AFR][1000 genomes]
rs62015498	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7168555	0.80[AFR][1000 genomes]
rs72741448	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv457202	chr15:73612377-73680301	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv569949	chr15:73612377-73680301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv524049	chr15:73612833-73680301	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3859015	TBC1D21	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73617800-73634600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:73621200-73632600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:73621200-73634000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:73622000-73634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:73622200-73630000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:73622200-73634400	Weak transcription	Brain Germinal Matrix	brain
7	chr15:73623000-73628000	Weak transcription	Fetal Brain Female	brain
8	chr15:73623200-73627000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:73623200-73627200	Weak transcription	Left Ventricle	heart
10	chr15:73623200-73627800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:73623200-73628000	Weak transcription	Right Atrium	heart
12	chr15:73623600-73627200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:73623600-73635400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:73623800-73632000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:73624000-73635400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:73624600-73635200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:73624600-73635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:73624800-73632400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:73624800-73632600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:73625800-73628000	Weak transcription	Spleen	Spleen
21	chr15:73626000-73637800	Enhancers	Fetal Heart	heart
22	chr15:73626400-73628800	Enhancers	Right Ventricle	heart

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