Variant report

Variant	rs6948583
Chromosome Location	chr7:103849940-103849941
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:103847130-103850285	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:103846910-103850210	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:103846892-103850163	K562	blood:	n/a	n/a
4	POLR2A	chr7:103847387-103849995	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:103628555..103630772-chr7:103847007..103849982,2	K562	blood:
2	chr7:103848404..103850130-chr7:104653038..104655393,2	MCF-7	breast:

Variant related genes	Relation type
ORC5	TF binding region
ENSG00000005483	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000189056	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10236259	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10236401	0.81[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10265732	0.86[AFR][1000 genomes]
rs10265960	0.86[AFR][1000 genomes]
rs10265985	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1035169	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10808128	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953407	0.88[AFR][1000 genomes]
rs10953408	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953409	0.87[AFR][1000 genomes]
rs10953410	0.87[AFR][1000 genomes]
rs113877	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11973848	0.86[AFR][1000 genomes]
rs11980573	0.86[AFR][1000 genomes]
rs12056186	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12056191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705180	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12705181	0.95[ASN][1000 genomes]
rs12705184	0.81[ASN][1000 genomes]
rs12705187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12705188	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12705190	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12705191	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12705192	0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12705193	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12705195	1.00[ASN][1000 genomes]
rs13230700	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs13238183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13438174	0.80[AFR][1000 genomes]
rs13438176	0.80[AFR][1000 genomes]
rs193888	0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs194837	0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194838	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194841	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs194846	0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194847	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194849	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[ASN][1000 genomes]
rs194851	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194857	0.85[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194858	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194859	0.84[ASN][1000 genomes]
rs194861	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194865	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs194867	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194868	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.84[ASN][1000 genomes]
rs2075219	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2075220	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2078807	1.00[YRI][hapmap]
rs2160397	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2188284	0.91[ASW][hapmap];1.00[YRI][hapmap]
rs2192965	0.83[YRI][hapmap]
rs2214009	1.00[YRI][hapmap]
rs2245659	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283035	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299408	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299409	0.88[ASN][1000 genomes]
rs2299411	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2385140	0.91[ASW][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28372965	0.81[AFR][1000 genomes]
rs3087358	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs34096272	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35034355	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3757734	0.96[ASN][1000 genomes]
rs3779518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808008	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3808009	0.83[ASN][1000 genomes]
rs3808010	0.84[ASN][1000 genomes]
rs3823979	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4140860	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265123	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4265124	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4286867	0.85[AFR][1000 genomes]
rs4370466	0.83[AFR][1000 genomes]
rs4370467	0.90[AFR][1000 genomes]
rs4385404	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4445159	0.87[AFR][1000 genomes]
rs4461830	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4486111	0.91[ASW][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs62485910	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6948440	0.90[AFR][1000 genomes]
rs6948673	0.88[AFR][1000 genomes]
rs6948723	0.90[AFR][1000 genomes]
rs6961262	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6962673	0.90[AFR][1000 genomes]
rs6967757	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6968451	0.90[AFR][1000 genomes]
rs765408	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7781828	0.94[ASN][1000 genomes]
rs9918581	1.00[YRI][hapmap]
rs9918639	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6948583	ZNHIT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103847600-103850000	Active TSS	Psoas Muscle	Psoas
2	chr7:103849000-103850200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:103849000-103850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:103849200-103850800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:103849600-103850400	Enhancers	Rectal Mucosa Donor 31	rectum

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