Variant report

Variant	rs9461340
Chromosome Location	chr6:27180046-27180047
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27178603..27181453-chr6:27860902..27863574,2	K562	blood:
2	chr6:27179126..27181346-chr6:27660529..27662958,2	K562	blood:

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11964003	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11964043	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13437191	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13437532	0.86[JPT][hapmap]
rs17739298	0.86[CEU][hapmap]
rs3800308	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800311	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs3800312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4145206	0.85[CEU][hapmap]
rs4711143	0.86[JPT][hapmap]
rs4711144	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713077	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5030957	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5030960	1.00[JPT][hapmap]
rs58336089	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6901448	0.85[ASN][1000 genomes]
rs6902483	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906761	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6912503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6918423	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6932243	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs73388532	0.86[ASN][1000 genomes]
rs7755577	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9393794	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468006	0.91[JPT][hapmap]
rs9468011	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468016	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.93[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv970092	chr6:27177750-27181734	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	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	chr6:27174400-27181400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:27177000-27181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:27177200-27181200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:27177200-27181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:27178000-27180600	Weak transcription	K562	blood
6	chr6:27178000-27181200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:27178000-27181400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:27178000-27181600	Weak transcription	GM12878-XiMat	blood
9	chr6:27179600-27182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:27180000-27181400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:27180000-27181400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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