Variant report

Variant	rs341917
Chromosome Location	chr5:77949565-77949566
allele	A/G
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:5)
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	CUX1	chr5:77949439-77949753	K562	blood:	n/a	n/a
2	RPC155	chr5:77949476-77949865	Hela-S3	cervix:	n/a	n/a
3	KAP1	chr5:77949554-77950219	U2OS	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:77949562..77953709-chr5:77953710..77956487,4	K562	blood:
2	chr5:77948053..77949941-chr5:77952156..77953774,2	K562	blood:
3	chr5:77943633..77945471-chr5:77948483..77951262,3	MCF-7	breast:
4	chr5:77947982..77950288-chr5:77962264..77964094,2	K562	blood:
5	chr5:77947585..77950288-chr5:77961353..77964094,3	K562	blood:

No data

Variant related genes	Relation type
LHFPL2	TF binding region
ENSG00000145685	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10060702	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163633	0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs168190	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs171035	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs189322	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs341918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341919	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs341920	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs341924	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs341925	0.92[ASN][1000 genomes]
rs341926	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs341927	0.92[ASN][1000 genomes]
rs341928	0.90[ASN][1000 genomes]
rs341930	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs344639	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461989	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522738	chr5:77434730-78063683	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3522739	chr5:77434730-78063683	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv949530	chr5:77830403-78477017	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv830356	chr5:77847022-78011999	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1021768	chr5:77881915-78465489	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2762527	chr5:77921199-78548196	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv1792242	chr5:77927033-77966625	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv528833	chr5:77937453-78016860	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1795250	chr5:77944003-77949565	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1846202	chr5:77944003-77949565	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:77945400-77949600	Weak transcription	Adipose Nuclei	Adipose
2	chr5:77945800-77952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:77945800-77962400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:77946000-77950800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:77946200-77949600	Weak transcription	Fetal Stomach	stomach
6	chr5:77946200-77950800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:77946200-77953600	Weak transcription	Ovary	ovary
8	chr5:77946600-77950200	Weak transcription	GM12878-XiMat	blood
9	chr5:77947000-77949800	Weak transcription	HepG2	liver
10	chr5:77948000-77950400	Enhancers	K562	blood
11	chr5:77949000-77949800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr5:77949000-77950600	Enhancers	Colon Smooth Muscle	Colon
13	chr5:77949000-77950600	Enhancers	Hela-S3	cervix
14	chr5:77949000-77951200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:77949200-77950000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:77949400-77949600	Enhancers	NHLF	lung
17	chr5:77949400-77949800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:77949400-77949800	Enhancers	Osteobl	bone
19	chr5:77949400-77950000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr5:77949400-77950400	Enhancers	HUVEC	blood vessel
21	chr5:77949400-77951200	Enhancers	A549	lung

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