Variant report

Variant	rs2465878
Chromosome Location	chr6:161318425-161318426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11970528	0.99[ASN][1000 genomes]
rs1247294	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247298	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247299	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1247300	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247302	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247305	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247307	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1247308	0.85[CEU][hapmap];0.93[JPT][hapmap]
rs1247309	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1247310	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247312	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1247313	0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247316	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247317	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247318	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247319	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247320	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247321	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247322	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247323	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1247325	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1247326	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1247327	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1247328	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1247329	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1247330	0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs1247360	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247361	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247362	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247363	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247364	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247365	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1663025	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1937474	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465834	0.87[JPT][hapmap]
rs2465869	0.97[ASN][1000 genomes]
rs2465870	0.99[ASN][1000 genomes]
rs2465871	0.97[ASN][1000 genomes]
rs2465876	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465877	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489955	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2489956	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2489962	0.87[ASN][1000 genomes]
rs62436898	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs935182	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs935183	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9355851	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9364580	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352911	chr6:161140543-161324358	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161311000-161320600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:161311000-161321000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:161313000-161321000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:161313200-161319000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:161316400-161320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:161316800-161320600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:161316800-161320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:161316800-161320800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:161316800-161320800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:161317000-161320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:161317000-161320800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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