Variant report

Variant	rs213241
Chromosome Location	chr6:28313020-28313021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:28312701-28313608	HepG2	liver:	n/a	n/a
2	SP1	chr6:28312903-28313375	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:28312905-28313440	HepG2	liver:	n/a	n/a
4	FOXA2	chr6:28312992-28313345	HepG2	liver:	n/a	n/a
5	ARID3A	chr6:28313002-28313283	HepG2	liver:	n/a	n/a
6	FOXA1	chr6:28312793-28313468	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:28312937-28313439	HepG2	liver:	n/a	n/a
8	FOXA1	chr6:28312977-28313477	HepG2	liver:	n/a	n/a
9	HDAC2	chr6:28312970-28313341	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28232695..28235468-chr6:28312123..28315031,2	K562	blood:
2	chr6:28301955..28305314-chr6:28311630..28316587,6	MCF-7	breast:
3	chr6:28106596..28109035-chr6:28311794..28313364,2	K562	blood:
4	chr6:28302467..28305224-chr6:28310834..28314742,3	MCF-7	breast:
5	chr6:28311214..28313624-chr6:28316114..28318164,2	MCF-7	breast:
6	chr6:28307801..28310523-chr6:28312557..28314569,2	MCF-7	breast:
7	chr6:28112424..28114351-chr6:28312409..28315217,2	K562	blood:
8	chr6:28283987..28285681-chr6:28312968..28315468,2	K562	blood:
9	chr6:28243132..28246086-chr6:28311018..28313357,3	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ZKSCAN3	TF binding region
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10456362	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1076639	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11751487	0.80[ASN][1000 genomes]
rs11755032	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755387	0.81[CHB][hapmap]
rs11965538	0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs13200462	1.00[JPT][hapmap]
rs1339899	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1419183	0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1679709	0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1679732	1.00[JPT][hapmap]
rs16894011	0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs1778507	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs1778508	0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1778511	1.00[JPT][hapmap]
rs17856167	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap]
rs1936365	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs213239	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]
rs213243	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];0.97[ASN][1000 genomes]
rs213244	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232427	0.81[CHB][hapmap]
rs2743554	0.82[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2799077	0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs2799079	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs6901575	0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6920512	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs73742521	0.89[EUR][1000 genomes]
rs853676	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853678	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853679	1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853681	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853682	0.83[ASN][1000 genomes]
rs853685	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853687	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.82[ASN][1000 genomes]
rs9295765	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs9380069	0.91[GIH][hapmap]
rs9393902	0.83[TSI][hapmap]
rs9393908	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9461446	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs9461448	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461449	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468321	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9468322	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs9468342	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468364	0.82[YRI][hapmap];0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213241	ZNF323	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
2	chr6:28304800-28317200	Weak transcription	Aorta	Aorta
3	chr6:28305000-28317200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:28305000-28317200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:28305200-28313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:28305200-28317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:28305200-28317000	Weak transcription	NHEK	skin
8	chr6:28305200-28317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:28305200-28317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:28305200-28317200	Weak transcription	HSMMtube	muscle
11	chr6:28305800-28317200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:28309400-28314800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:28312200-28314000	Enhancers	HepG2	liver
14	chr6:28312600-28313800	Enhancers	K562	blood

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