Variant report

Variant	rs2248386
Chromosome Location	chr6:31011247-31011248
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31007765..31010643-chr6:31011051..31014483,3	K562	blood:
2	chr6:30930448..30932283-chr6:31010953..31013898,2	K562	blood:
3	chr6:30880584..30886230-chr6:31009556..31012955,9	MCF-7	breast:
4	chr6:31010612..31011425-chr6:31055068..31055590,2	K562	blood:
5	chr6:30883250..30883934-chr6:31010475..31011616,5	MCF-7	breast:
6	chr6:31010707..31012864-chr6:31028593..31030504,2	MCF-7	breast:
7	chr6:31010735..31013571-chr6:31016470..31018721,2	MCF-7	breast:
8	chr6:30851860..30853560-chr6:31009534..31012397,2	MCF-7	breast:
9	chr6:30882943..30883998-chr6:31010336..31011408,3	MCF-7	breast:
10	chr6:31010860..31013816-chr6:31025922..31027807,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2508015	0.85[AFR][1000 genomes]
rs2517536	0.83[ASN][1000 genomes]
rs2523867	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523875	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2523877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844645	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844647	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131926	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2248386	C6orf1	cis	parietal	SCAN
rs2248386	HIST1H3J	cis	parietal	SCAN
rs2248386	hmm31752	cis	multi-tissue	Pritchard
rs2248386	PRSS16	cis	cerebellum	SCAN
rs2248386	ZKSCAN4	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr6:31010800-31011400	Enhancers	Brain Hippocampus Middle	brain
6	chr6:31010800-31011400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr6:31010800-31011600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:31010800-31011600	Enhancers	NHDF-Ad	bronchial
9	chr6:31010800-31011800	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:31011000-31011400	Enhancers	Primary B cells from cord blood	blood
11	chr6:31011000-31011600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:31011000-31011600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:31011000-31011600	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:31011000-31011600	Enhancers	Adipose Nuclei	Adipose
15	chr6:31011000-31011600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr6:31011000-31014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:31011000-31015800	Weak transcription	Hela-S3	cervix
18	chr6:31011200-31011400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:31011200-31011400	Enhancers	GM12878-XiMat	blood
20	chr6:31011200-31011600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr6:31011200-31011600	Enhancers	Monocytes-CD14+_RO01746	blood

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