Variant report

Variant	rs3800308
Chromosome Location	chr6:27201262-27201263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27197426..27201736-chr6:27203200..27207154,7	K562	blood:
2	chr6:27200503..27203142-chr6:27342882..27344884,2	K562	blood:
3	chr6:27199807..27202562-chr6:27760063..27762279,2	MCF-7	breast:
4	chr6:27197041..27202373-chr6:27261458..27267425,7	K562	blood:
5	chr6:27195411..27200167-chr6:27200252..27206108,10	K562	blood:
6	chr6:27201132..27202809-chr6:27205095..27206707,2	MCF-7	breast:

Extended variants
information (count: 32 )
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];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964043	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437191	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13437532	0.87[JPT][hapmap]
rs17739298	0.86[CEU][hapmap]
rs3800311	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3800312	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145206	0.86[CEU][hapmap]
rs4711143	0.87[JPT][hapmap]
rs4711144	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713074	0.87[GIH][hapmap]
rs4713075	0.86[EUR][1000 genomes]
rs4713077	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030957	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030960	1.00[JPT][hapmap]
rs58336089	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902483	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6906761	0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs6912503	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918423	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468006	0.91[JPT][hapmap]
rs9468011	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468015	0.87[GIH][hapmap]
rs9468016	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3800308	HIST1H4C	cis	parietal	SCAN
rs3800308	HIST1H2AL	cis	cerebellum	SCAN
rs3800308	ZNF192	cis	parietal	SCAN
rs3800308	NKAPL	cis	parietal	SCAN
rs3800308	ZNF204P	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27198800-27202600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:27198800-27202600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:27198800-27202600	Weak transcription	GM12878-XiMat	blood
4	chr6:27198800-27202600	Weak transcription	HMEC	breast
5	chr6:27198800-27203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:27199000-27202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:27199000-27205600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:27199400-27201800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:27199400-27201800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:27199400-27202400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:27199400-27202400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:27199400-27202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:27199600-27201400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:27199600-27201800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:27199600-27202000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:27199600-27202400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:27199600-27202600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:27199600-27202800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:27199600-27202800	Weak transcription	HepG2	liver
20	chr6:27199800-27201800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:27199800-27202800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:27200200-27202800	Weak transcription	A549	lung
23	chr6:27200400-27202000	Weak transcription	K562	blood

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