Variant report

Variant	rs11150596
Chromosome Location	chr16:30850242-30850243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30849028..30850619-chr16:30884985..30886690,2	MCF-7	breast:
2	chr16:30849738..30852527-chr16:30907095..30908928,2	K562	blood:
3	chr16:30787386..30789402-chr16:30849116..30851160,2	MCF-7	breast:
4	chr16:30843974..30846904-chr16:30847751..30850553,2	K562	blood:

Variant related genes	Relation type
ENSG00000260083	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000150281	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046276	0.82[CEU][hapmap]
rs10782001	0.82[CEU][hapmap]
rs10782002	0.82[CEU][hapmap]
rs11150599	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap]
rs11150600	0.82[CEU][hapmap]
rs11640534	0.82[CEU][hapmap]
rs11647697	0.84[ASN][1000 genomes]
rs11864054	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12447534	0.81[EUR][1000 genomes]
rs12924903	0.82[CEU][hapmap]
rs12926237	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12926295	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs12928852	0.82[CEU][hapmap]
rs12929065	0.84[ASN][1000 genomes]
rs12930944	0.84[ASN][1000 genomes]
rs13337900	0.89[EUR][1000 genomes]
rs13338946	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs1458202	0.82[CEU][hapmap]
rs2125293	0.84[ASN][1000 genomes]
rs2168834	0.84[ASN][1000 genomes]
rs2289442	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2335013	0.84[ASN][1000 genomes]
rs28421305	0.95[ASN][1000 genomes]
rs35629860	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3747481	0.82[CHD][hapmap]
rs3747486	0.88[CHD][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap]
rs3812999	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.91[YRI][hapmap]
rs4889489	0.82[EUR][1000 genomes]
rs4889490	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4889534	0.84[ASN][1000 genomes]
rs4889536	0.84[ASN][1000 genomes]
rs4889614	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4889622	0.84[ASN][1000 genomes]
rs4889627	0.87[ASN][1000 genomes]
rs4889630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4889651	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4889653	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs62057223	0.81[EUR][1000 genomes]
rs6565207	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7187359	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs7192475	0.87[EUR][1000 genomes]
rs7198250	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs7206511	0.82[CEU][hapmap]
rs72799316	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73524556	0.89[EUR][1000 genomes]
rs7500719	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8046001	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8046391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8050330	0.89[EUR][1000 genomes]
rs8050588	0.82[CEU][hapmap]
rs8058578	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs8058961	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs8063565	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs885107	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9319587	0.95[ASN][1000 genomes]
rs9319588	0.82[CEU][hapmap]
rs9932572	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933843	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap]
rs9933875	0.87[EUR][1000 genomes]
rs9934249	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9938088	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv1060384	chr16:30802415-30878838	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1059633	chr16:30803099-30867916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
13	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11150596	MYST1	cis	cerebellum	SCAN
rs11150596	PHKG2	cis	parietal	SCAN
rs11150596	ITGAX	cis	parietal	SCAN
rs11150596	BCL7C	cis	cerebellum	SCAN
rs11150596	MYST1	cis	parietal	SCAN
rs11150596	RABEP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30836000-30850600	Weak transcription	Esophagus	oesophagus
2	chr16:30840200-30856400	Weak transcription	Aorta	Aorta
3	chr16:30841000-30856200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr16:30841000-30858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:30841200-30851000	Weak transcription	Brain Substantia Nigra	brain
6	chr16:30841400-30856200	Weak transcription	Left Ventricle	heart
7	chr16:30842200-30850800	Weak transcription	HSMMtube	muscle
8	chr16:30842600-30856200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr16:30844200-30855800	Weak transcription	Fetal Kidney	kidney
10	chr16:30844200-30856200	Weak transcription	Primary T cells from cord blood	blood
11	chr16:30844200-30856400	Weak transcription	Gastric	stomach
12	chr16:30844400-30856000	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:30845600-30850600	Weak transcription	Fetal Lung	lung
14	chr16:30845600-30850800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:30845600-30856200	Weak transcription	Adipose Nuclei	Adipose
16	chr16:30845600-30856200	Weak transcription	Brain Anterior Caudate	brain
17	chr16:30845800-30884800	Weak transcription	Brain Germinal Matrix	brain
18	chr16:30846200-30856200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:30846200-30856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr16:30846200-30856400	Weak transcription	Ovary	ovary
21	chr16:30846200-30863000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:30846400-30856200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr16:30846400-30856200	Weak transcription	Brain Hippocampus Middle	brain
24	chr16:30846400-30856400	Weak transcription	Lung	lung
25	chr16:30846400-30883400	Weak transcription	Fetal Brain Female	brain
26	chr16:30846600-30856200	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:30846600-30856400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr16:30846800-30851000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:30846800-30856200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr16:30846800-30885600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr16:30847000-30856200	Weak transcription	Fetal Stomach	stomach
32	chr16:30849000-30850800	Enhancers	Fetal Intestine Small	intestine
33	chr16:30849000-30852400	Enhancers	Stomach Mucosa	stomach
34	chr16:30849000-30852600	Enhancers	Fetal Intestine Large	intestine
35	chr16:30849200-30851200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr16:30849400-30850400	Weak transcription	Pancreas	Pancrea
37	chr16:30849400-30850600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr16:30849400-30850600	Weak transcription	A549	lung
39	chr16:30849400-30850800	Enhancers	Duodenum Mucosa	Duodenum
40	chr16:30849400-30856200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr16:30849600-30850400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr16:30849600-30850600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr16:30849600-30850600	Weak transcription	Hela-S3	cervix
44	chr16:30849600-30851000	Weak transcription	Placenta	Placenta
45	chr16:30849600-30856200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:30849800-30855600	Weak transcription	K562	blood
47	chr16:30849800-30856200	Weak transcription	Brain Angular Gyrus	brain
48	chr16:30850200-30850600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr16:30850200-30850800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr16:30850200-30851400	Flanking Active TSS	HepG2	liver

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