Variant report

Variant	rs2523872
Chromosome Location	chr6:31012730-31012731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31007765..31010643-chr6:31011051..31014483,3	K562	blood:
2	chr6:30883696..30885224-chr6:31012672..31014658,2	MCF-7	breast:
3	chr6:30883355..30884929-chr6:31011755..31013954,2	K562	blood:
4	chr6:30930448..30932283-chr6:31010953..31013898,2	K562	blood:
5	chr6:30880584..30886230-chr6:31009556..31012955,9	MCF-7	breast:
6	chr6:31010707..31012864-chr6:31028593..31030504,2	MCF-7	breast:
7	chr6:30883032..30883759-chr6:31011810..31012818,4	MCF-7	breast:
8	chr6:31010735..31013571-chr6:31016470..31018721,2	MCF-7	breast:
9	chr6:31010860..31013816-chr6:31025922..31027807,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs2251825	0.84[AFR][1000 genomes]
rs2394428	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2394429	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394430	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517527	0.81[EUR][1000 genomes]
rs2517532	0.84[AFR][1000 genomes]
rs2517533	0.84[AFR][1000 genomes]
rs2517534	0.81[AFR][1000 genomes]
rs2517538	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517539	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517543	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517548	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517550	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517551	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2517552	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517553	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523856	0.81[EUR][1000 genomes]
rs2523858	0.84[AFR][1000 genomes]
rs2523862	0.84[AFR][1000 genomes]
rs2523870	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523873	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523874	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844645	0.80[ASN][1000 genomes]
rs2844665	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844669	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844672	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844681	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844683	0.84[EUR][1000 genomes]
rs3131927	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	esv3489797	chr6:31012377-31013068	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3489798	chr6:31012377-31013068	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv823474	chr6:31012507-31013022	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3411233	chr6:31012552-31013614	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2327814	chr6:31012659-31013146	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2523872	HLA-B	Cis_1M	lymphoblastoid	RTeQTL
rs2523872	TCF19	Cis_1M	lymphoblastoid	RTeQTL
rs2523872	ZNF187	cis	cerebellum	SCAN
rs2523872	HCG22	cis	lymphoblastoid	seeQTL
rs2523872	HLA-C	cis	lymphoblastoid	GTEx
rs2523872	C6orf1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31006000-31014800	Weak transcription	Right Atrium	heart
2	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:31010200-31015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:31010600-31021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:31011000-31014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:31011000-31015800	Weak transcription	Hela-S3	cervix

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