Variant report

Variant	rs6933400
Chromosome Location	chr6:30907176-30907177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr6:30907135-30907763	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr6:30907085-30907859	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr6:30906401-30907957	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30887279..30890468-chr6:30905841..30907751,3	K562	blood:
2	chr6:30902336..30907569-chr6:30907613..30911595,7	K562	blood:
3	chr6:30885492..30888779-chr6:30905268..30908318,3	K562	blood:
4	chr6:30896359..30898136-chr6:30906028..30908064,2	K562	blood:

No data

Variant related genes	Relation type
DPCR1	TF binding region
ENSG00000168631	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11970154	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2253705	0.89[AFR][1000 genomes]
rs2517459	0.87[AFR][1000 genomes]
rs2532932	0.89[AFR][1000 genomes]
rs3130779	0.86[AFR][1000 genomes]
rs3130788	0.81[AFR][1000 genomes]
rs3131032	0.86[AFR][1000 genomes]
rs3131034	0.85[AFR][1000 genomes]
rs3891155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56366011	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58893284	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59417026	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73432206	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv462743	chr6:30905313-30957766	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv601483	chr6:30905313-30957766	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6933400	PRSS16	cis	cerebellum	SCAN
rs6933400	HIST1H2AJ	cis	cerebellum	SCAN
rs6933400	SPDEF	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30897000-30909800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:30904200-30910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:30904200-30910200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:30904400-30907600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:30905000-30907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:30905200-30910200	Weak transcription	Right Ventricle	heart
7	chr6:30905400-30907600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:30905600-30909000	Enhancers	Esophagus	oesophagus
9	chr6:30905800-30908600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:30906000-30908600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:30906200-30907400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:30906200-30907800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:30906400-30907800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:30906400-30908600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:30906400-30909600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:30906600-30907600	Weak transcription	Pancreas	Pancrea
17	chr6:30906600-30907800	Enhancers	HMEC	breast
18	chr6:30906600-30909600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:30906600-30910200	Weak transcription	Lung	lung
20	chr6:30906800-30907200	Flanking Active TSS	Stomach Mucosa	stomach

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