Variant report

Variant	rs551238
Chromosome Location	chr7:100321528-100321529
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100315279..100318194-chr7:100320126..100322658,3	K562	blood:
2	chr7:100314177..100318194-chr7:100318771..100321626,3	K562	blood:
3	chr7:100315257..100318069-chr7:100320272..100323098,2	MCF-7	breast:
4	chr7:100319576..100322114-chr7:100397770..100400557,3	MCF-7	breast:
5	chr7:100288252..100292867-chr7:100319528..100322364,4	K562	blood:
6	chr7:100302553..100308135-chr7:100314195..100322207,16	MCF-7	breast:
7	chr7:100302051..100306591-chr7:100312993..100321692,11	MCF-7	breast:
8	chr7:100291635..100293380-chr7:100321369..100322955,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172336	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10277087	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953301	0.89[JPT][hapmap]
rs11520986	0.89[JPT][hapmap]
rs11974395	0.89[JPT][hapmap]
rs11979818	0.89[JPT][hapmap]
rs11983334	0.89[JPT][hapmap]
rs1617640	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1734908	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1734909	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1734910	0.94[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2075672	0.86[MEX][hapmap]
rs221771	0.95[EUR][1000 genomes]
rs221772	0.95[EUR][1000 genomes]
rs221788	0.85[EUR][1000 genomes]
rs221790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs221795	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs221801	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs2272572	0.89[JPT][hapmap]
rs2432930	0.96[EUR][1000 genomes]
rs4727459	0.89[JPT][hapmap]
rs4729597	0.91[MEX][hapmap]
rs4729602	0.89[JPT][hapmap]
rs4729606	0.89[JPT][hapmap]
rs4729607	0.89[JPT][hapmap]
rs475339	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs504141	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs507392	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554055	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568733	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576236	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829284	chr7:100318927-100337055	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3519627	chr7:100320350-100343994	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3519628	chr7:100320350-100343994	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs551238	C10orf107	trans	parietal	SCAN
rs551238	TAC1	cis	parietal	SCAN
rs551238	POLR2J	cis	parietal	SCAN
rs551238	DLX5	cis	cerebellum	SCAN
rs551238	MEPCE	cis	cerebellum	SCAN
rs551238	TSC22D4	cis	parietal	SCAN
rs551238	PILRB	cis	cerebellum	SCAN
rs551238	MOSPD3	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100319200-100342800	Weak transcription	Right Atrium	heart
2	chr7:100320000-100322800	Weak transcription	Placenta	Placenta
3	chr7:100320200-100322800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:100320400-100321800	Flanking Active TSS	Pancreas	Pancrea
5	chr7:100320400-100322200	Flanking Active TSS	Liver	Liver
6	chr7:100321400-100321600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:100321400-100321600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:100321400-100321600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:100321400-100321600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:100321400-100321600	Bivalent Enhancer	Fetal Stomach	stomach
11	chr7:100321400-100322000	Flanking Active TSS	HepG2	liver

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