Variant report

Variant	rs3800312
Chromosome Location	chr6:27210614-27210615
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	TCF7L2	chr6:27210454-27212017	HEK293	kidney:	n/a	n/a
2	CEBPB	chr6:27210588-27211061	A549	lung:	n/a	chr6:27210854-27210863 chr6:27210854-27210863 chr6:27210852-27210863 chr6:27210854-27210863
3	POLR2A	chr6:27208304-27211412	K562	blood:	n/a	n/a
4	CTCF	chr6:27210540-27210690	HFF-Myc	foreskin:	n/a	n/a
5	TEAD4	chr6:27210320-27210734	K562	blood:	n/a	n/a
6	KAP1	chr6:27210612-27211439	U2OS	brain:	n/a	n/a
7	CTCF	chr6:27210540-27210690	A549	lung:	n/a	n/a
8	TEAD4	chr6:27210330-27210997	K562	blood:	n/a	n/a
9	CTCF	chr6:27210540-27210690	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27208172..27214279-chr6:27217175..27221037,5	MCF-7	breast:
2	chr6:27208791..27211821-chr6:27212133..27214069,3	K562	blood:
3	chr6:27112441..27115377-chr6:27208801..27210793,2	K562	blood:
4	chr6:27203954..27208601-chr6:27209090..27212437,6	K562	blood:

Variant related genes	Relation type
PRSS16	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000112812	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11964003	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437191	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13437532	0.87[JPT][hapmap]
rs17739298	0.86[CEU][hapmap]
rs3800308	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800311	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3800313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145206	0.86[CEU][hapmap]
rs4711143	0.87[JPT][hapmap]
rs4711144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713074	0.87[GIH][hapmap]
rs4713075	0.88[EUR][1000 genomes]
rs4713077	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030957	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030960	1.00[JPT][hapmap]
rs58336089	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902483	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6906761	0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs6912503	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918423	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6932243	0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs7755577	0.92[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs9393794	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468006	0.91[JPT][hapmap]
rs9468011	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468015	0.87[GIH][hapmap]
rs9468016	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3800312	HIST1H4C	cis	parietal	SCAN
rs3800312	ZNF204P	cis	cerebellum	SCAN
rs3800312	NKAPL	cis	parietal	SCAN
rs3800312	ZNF192	cis	parietal	SCAN
rs3800312	HIST1H2AL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27207000-27212200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27210400-27211000	Enhancers	K562	blood
3	chr6:27210600-27210800	Bivalent Enhancer	HepG2	liver

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