Variant report

Variant	rs11864054
Chromosome Location	chr16:30846134-30846135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30835263..30837904-chr16:30846097..30849044,3	K562	blood:
2	chr16:30838714..30840881-chr16:30843458..30846272,2	MCF-7	breast:
3	chr16:30786121..30788746-chr16:30845072..30846818,3	K562	blood:
4	chr16:30845280..30847524-chr16:30884857..30888269,3	MCF-7	breast:
5	chr16:30843974..30846904-chr16:30847751..30850553,2	K562	blood:

Variant related genes	Relation type
ENSG00000265991	Chromatin interaction
ENSG00000260083	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11150596	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11150599	0.82[CHB][hapmap]
rs11640961	1.00[ASW][hapmap]
rs11647697	0.84[ASN][1000 genomes]
rs11649653	1.00[ASW][hapmap]
rs12926237	0.82[CHB][hapmap];0.95[ASN][1000 genomes]
rs12926295	0.82[CHB][hapmap]
rs12929065	0.84[ASN][1000 genomes]
rs12930944	0.84[ASN][1000 genomes]
rs13338946	0.88[CHD][hapmap]
rs2125293	0.84[ASN][1000 genomes]
rs2168834	0.84[ASN][1000 genomes]
rs2289442	0.88[CHD][hapmap]
rs2335013	0.84[ASN][1000 genomes]
rs28421305	0.95[ASN][1000 genomes]
rs35629860	0.88[CHD][hapmap]
rs3747481	0.82[CHD][hapmap]
rs3747486	0.88[CHD][hapmap]
rs3812999	0.88[CHD][hapmap]
rs4889490	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4889534	0.84[ASN][1000 genomes]
rs4889536	0.84[ASN][1000 genomes]
rs4889603	1.00[ASW][hapmap]
rs4889614	0.81[ASN][1000 genomes]
rs4889622	0.84[ASN][1000 genomes]
rs4889627	0.87[ASN][1000 genomes]
rs4889630	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs4889651	0.82[CHB][hapmap]
rs4889653	0.82[CHB][hapmap]
rs62057232	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6565207	0.85[ASN][1000 genomes]
rs7187359	0.88[CHD][hapmap];0.95[MKK][hapmap]
rs7198250	0.88[CHD][hapmap]
rs7500719	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[ASN][1000 genomes]
rs8046001	0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs8046391	0.82[CHB][hapmap];0.95[ASN][1000 genomes]
rs8046707	1.00[ASW][hapmap]
rs8058578	0.88[CHD][hapmap]
rs8058961	0.88[CHD][hapmap]
rs8063565	0.82[CHB][hapmap]
rs885107	0.88[CHD][hapmap];0.90[MKK][hapmap]
rs9319587	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9932572	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs9933843	0.82[CHB][hapmap]
rs9934249	0.95[ASN][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11864054	ZNF668	cis	cerebellum	SCAN
rs11864054	MYST1	cis	parietal	SCAN
rs11864054	C16orf93	cis	parietal	SCAN
rs11864054	LAT	cis	parietal	SCAN
rs11864054	SETD1A	cis	parietal	SCAN
rs11864054	STX1B	cis	cerebellum	SCAN
rs11864054	BOLA2	cis	lymphoblastoid	seeQTL
rs11864054	YPEL3	cis	cerebellum	SCAN
rs11864054	MYST1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30836000-30850600	Weak transcription	Esophagus	oesophagus
2	chr16:30837200-30849000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr16:30840200-30856400	Weak transcription	Aorta	Aorta
4	chr16:30841000-30856200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr16:30841000-30858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:30841200-30851000	Weak transcription	Brain Substantia Nigra	brain
7	chr16:30841400-30856200	Weak transcription	Left Ventricle	heart
8	chr16:30842200-30849000	Weak transcription	Fetal Intestine Large	intestine
9	chr16:30842200-30850800	Weak transcription	HSMMtube	muscle
10	chr16:30842600-30856200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:30843400-30849000	Weak transcription	Placenta	Placenta
12	chr16:30844200-30855800	Weak transcription	Fetal Kidney	kidney
13	chr16:30844200-30856200	Weak transcription	Primary T cells from cord blood	blood
14	chr16:30844200-30856400	Weak transcription	Gastric	stomach
15	chr16:30844400-30856000	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:30844600-30846200	Strong transcription	Ovary	ovary
17	chr16:30844600-30846400	Strong transcription	Fetal Brain Female	brain
18	chr16:30844600-30847000	Strong transcription	Fetal Stomach	stomach
19	chr16:30844600-30848200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:30844800-30846200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:30844800-30846600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr16:30844800-30846600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr16:30844800-30846600	Strong transcription	Fetal Muscle Leg	muscle
24	chr16:30844800-30846800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr16:30845000-30846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr16:30845200-30846200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr16:30845400-30846200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:30845400-30846400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:30845400-30846400	Strong transcription	Brain Hippocampus Middle	brain
30	chr16:30845400-30846400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr16:30845400-30846400	Strong transcription	Lung	lung
32	chr16:30845400-30846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:30845400-30846800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:30845400-30849600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr16:30845600-30846200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:30845600-30849000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:30845600-30850600	Weak transcription	Fetal Lung	lung
38	chr16:30845600-30850800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr16:30845600-30856200	Weak transcription	Adipose Nuclei	Adipose
40	chr16:30845600-30856200	Weak transcription	Brain Anterior Caudate	brain
41	chr16:30845800-30849000	Weak transcription	Fetal Intestine Small	intestine
42	chr16:30845800-30849000	Weak transcription	Right Ventricle	heart
43	chr16:30845800-30884800	Weak transcription	Brain Germinal Matrix	brain

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