Variant report

Variant	rs8058578
Chromosome Location	chr16:30726248-30726249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30717656..30719945-chr16:30724510..30726621,2	K562	blood:
2	chr16:30669250..30670899-chr16:30724875..30726611,2	MCF-7	breast:
3	chr16:30723897..30726651-chr16:30727280..30729745,2	MCF-7	breast:
4	chr16:30726174..30728075-chr16:30787184..30789746,3	K562	blood:
5	chr16:30707422..30715768-chr16:30721242..30729414,24	MCF-7	breast:
6	chr16:30724388..30726309-chr16:30728626..30730137,2	K562	blood:
7	chr16:30708760..30712474-chr16:30717976..30728042,17	K562	blood:

Variant related genes	Relation type
ENSG00000080603	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000222287	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11150596	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs11864054	0.88[CHD][hapmap]
rs12918327	0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs12926237	0.86[JPT][hapmap]
rs13338946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35629860	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35969813	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747481	0.94[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747486	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3812999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs4616297	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889490	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4889614	0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs4889630	0.86[JPT][hapmap]
rs4889651	0.81[GIH][hapmap]
rs4889653	0.81[GIH][hapmap]
rs6565201	0.88[EUR][1000 genomes]
rs67128646	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67456513	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186852	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs7187359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197475	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs7197770	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs7204278	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7500719	0.88[ASW][hapmap];0.94[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs8046001	0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs8046391	0.94[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs8048448	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051050	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055315	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055661	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8058928	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058961	0.94[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs885107	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9925025	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs9928572	0.84[EUR][1000 genomes]
rs9932572	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8058578	MYST1	cis	parietal	SCAN
rs8058578	ITGAX	cis	parietal	SCAN
rs8058578	RNF40	cis	cerebellum	SCAN
rs8058578	ZNF768	cis	parietal	SCAN
rs8058578	MYST1	cis	cerebellum	SCAN
rs8058578	C16orf93	cis	parietal	SCAN
rs8058578	PHKG2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30711400-30751400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:30711400-30757000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr16:30711600-30727200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:30711600-30735600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr16:30711600-30735800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:30711600-30736000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:30711600-30738000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:30711600-30738800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr16:30711600-30750800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr16:30711600-30752000	Strong transcription	Fetal Lung	lung
11	chr16:30711600-30756200	Strong transcription	Thymus	Thymus
12	chr16:30711800-30732200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr16:30711800-30737000	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr16:30711800-30738400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr16:30711800-30738400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:30711800-30739000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr16:30711800-30739200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr16:30711800-30739600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr16:30711800-30757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:30711800-30757200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:30712000-30736800	Strong transcription	Fetal Brain Female	brain
22	chr16:30712000-30737200	Strong transcription	HSMMtube	muscle
23	chr16:30712000-30756600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr16:30712200-30726400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr16:30712200-30726600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr16:30712200-30727000	Strong transcription	Adipose Nuclei	Adipose
27	chr16:30712200-30727200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:30712200-30729400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:30712200-30733400	Strong transcription	Spleen	Spleen
30	chr16:30712200-30735400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr16:30712200-30735600	Strong transcription	Fetal Intestine Large	intestine
32	chr16:30712200-30735800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:30712200-30735800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:30712200-30736400	Strong transcription	Colon Smooth Muscle	Colon
35	chr16:30712200-30736800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr16:30712200-30737000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr16:30712200-30737400	Strong transcription	Lung	lung
38	chr16:30712200-30754200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr16:30712200-30755000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr16:30712200-30757400	Strong transcription	Fetal Stomach	stomach
41	chr16:30712200-30758800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr16:30712400-30726400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr16:30712400-30728400	Strong transcription	HepG2	liver
44	chr16:30712400-30735000	Strong transcription	Liver	Liver
45	chr16:30712400-30736400	Strong transcription	Fetal Intestine Small	intestine
46	chr16:30712400-30736800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:30712400-30751200	Strong transcription	Left Ventricle	heart
48	chr16:30712400-30751600	Strong transcription	Fetal Muscle Leg	muscle
49	chr16:30712600-30727000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr16:30712600-30729000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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