Variant report

Variant	rs3800314
Chromosome Location	chr6:27236048-27236049
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27228304..27231014-chr6:27236000..27238035,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10946904	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1156086	0.82[ASN][1000 genomes]
rs2295603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393915	0.83[MEX][hapmap]
rs28594674	0.83[ASN][1000 genomes]
rs2893911	0.81[CEU][hapmap]
rs3800309	0.83[ASN][1000 genomes]
rs3800319	0.81[CEU][hapmap]
rs4236043	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4546474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4559087	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs4713074	0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs5030956	0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6902268	0.82[ASN][1000 genomes]
rs6916555	0.82[ASN][1000 genomes]
rs6917311	0.83[ASN][1000 genomes]
rs6940384	0.83[ASN][1000 genomes]
rs7746841	0.80[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs9366689	0.81[CEU][hapmap]
rs9368501	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap]
rs9379968	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9468009	0.80[ASN][1000 genomes]
rs9468010	0.81[ASN][1000 genomes]
rs9468013	0.82[ASN][1000 genomes]
rs9468015	0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs996247	0.82[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3800314	HMGN4	cis	lymphoblastoid	seeQTL
rs3800314	BTN3A2	cis	lymphoblastoid	seeQTL
rs3800314	ZSCAN23	cis	cerebellum	SCAN
rs3800314	HIST1H2BM	cis	cerebellum	SCAN
rs3800314	ZKSCAN3	cis	parietal	SCAN
rs3800314	BTN3A3	cis	cerebellum	SCAN
rs3800314	ZNF323	cis	parietal	SCAN
rs3800314	ZNF204P	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27232000-27236400	Weak transcription	K562	blood
2	chr6:27235600-27236400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27235800-27236200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:27235800-27236200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27235800-27236200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:27235800-27236200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:27235800-27236200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:27235800-27236200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:27235800-27236200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:27235800-27236200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:27235800-27236200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:27235800-27236200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:27235800-27236200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:27235800-27236200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:27235800-27236200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:27235800-27236400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:27236000-27236200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27236000-27236200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr6:27236000-27236200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:27236000-27236200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr6:27236000-27236200	Bivalent/Poised TSS	Fetal Heart	heart
22	chr6:27236000-27236200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr6:27236000-27236200	Bivalent/Poised TSS	NHEK	skin

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