Variant report

Variant	rs377514
Chromosome Location	chr6:28491950-28491951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:28491936-28491965	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28490091..28492168-chr6:28493727..28495713,2	MCF-7	breast:
2	chr6:28490306..28492074-chr6:28498929..28501971,3	K562	blood:
3	chr6:28490306..28492074-chr6:28498929..28501092,2	K562	blood:

Variant related genes	Relation type
GPX5	TF binding region
ENSG00000224586	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1003359	0.87[ASN][1000 genomes]
rs12661782	1.00[CEU][hapmap];0.91[CHD][hapmap];0.83[EUR][1000 genomes]
rs16894139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064424	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2071966	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2078035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078439	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191037	0.92[ASN][1000 genomes]
rs2227228	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2273106	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2531822	0.82[ASN][1000 genomes]
rs28382604	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2859355	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2859356	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs2859358	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35327256	0.83[EUR][1000 genomes]
rs35921765	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs380879	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs392230	0.82[AMR][1000 genomes]
rs406113	0.83[ASN][1000 genomes]
rs434112	0.83[ASN][1000 genomes]
rs440481	0.93[ASN][1000 genomes]
rs445870	0.87[ASN][1000 genomes]
rs448450	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451774	0.82[ASN][1000 genomes]
rs4713166	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4713167	0.87[ASN][1000 genomes]
rs62402370	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6456822	0.87[ASN][1000 genomes]
rs6456823	0.87[ASN][1000 genomes]
rs6921021	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72844230	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs769189	0.87[EUR][1000 genomes]
rs7743046	0.87[ASN][1000 genomes]
rs7759252	0.86[ASN][1000 genomes]
rs9468385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974334	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs377514	HIST1H2BB	cis	cerebellum	SCAN
rs377514	BTN2A3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28489600-28492200	Enhancers	Primary T cells from cord blood	blood
2	chr6:28490000-28493600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:28491400-28492400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:28491400-28493000	Weak transcription	K562	blood
5	chr6:28491400-28493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:28491600-28493000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:28491600-28493000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:28491600-28493000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:28491600-28493000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:28491600-28493200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:28491600-28493400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:28491800-28493200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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