Variant report

Variant	rs3747481
Chromosome Location	chr16:30666367-30666368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30666163-30666973	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30665738..30673826-chr16:30707321..30713630,33	K562	blood:
2	chr16:30665347..30684079-chr16:30697204..30714344,66	MCF-7	breast:
3	chr16:30455506..30458310-chr16:30666294..30667926,2	K562	blood:

Variant related genes	Relation type
FBRS	TF binding region
PRR14	TF binding region
ENSG00000080603	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000222287	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11150596	0.82[CHD][hapmap]
rs11864054	0.82[CHD][hapmap]
rs12918327	0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs13338946	0.94[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289442	0.94[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35629860	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35969813	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747486	0.82[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap]
rs3812999	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4616297	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4889490	0.94[CHD][hapmap]
rs4889614	0.92[GIH][hapmap];0.85[TSI][hapmap]
rs6565201	0.81[EUR][1000 genomes]
rs67128646	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67456513	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7186852	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs7187359	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7197475	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs7197770	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7198250	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7204278	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7500719	0.94[ASW][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap]
rs8046001	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs8046391	0.82[YRI][hapmap]
rs8048448	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051050	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055315	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8055661	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8058578	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]
rs8058928	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8058961	0.89[ASW][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap]
rs885107	0.82[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925025	0.94[CHD][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3747481	C16orf93	cis	parietal	SCAN
rs3747481	PHKG2	cis	parietal	SCAN
rs3747481	ITGAX	cis	parietal	SCAN
rs3747481	MYST1	cis	parietal	SCAN
rs3747481	RNF40	cis	cerebellum	SCAN
rs3747481	ZNF768	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30663600-30668400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr16:30663600-30668800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:30663800-30666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr16:30663800-30667400	Strong transcription	Esophagus	oesophagus
5	chr16:30663800-30667600	Strong transcription	Ovary	ovary
6	chr16:30663800-30668000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:30663800-30668000	Strong transcription	Thymus	Thymus
8	chr16:30663800-30668200	Strong transcription	Primary T cells from cord blood	blood
9	chr16:30664000-30666600	Weak transcription	A549	lung
10	chr16:30664000-30666600	Weak transcription	HSMMtube	muscle
11	chr16:30664000-30666800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:30664000-30667200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:30664000-30667400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr16:30664000-30667400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr16:30664000-30667600	Strong transcription	Aorta	Aorta
16	chr16:30664000-30667800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr16:30664000-30667800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:30664000-30667800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr16:30664000-30668000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr16:30664000-30668000	Strong transcription	Fetal Intestine Large	intestine
21	chr16:30664000-30668000	Strong transcription	NHLF	lung
22	chr16:30664000-30668000	Strong transcription	Osteobl	bone
23	chr16:30664000-30668200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:30664000-30668200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr16:30664000-30668200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr16:30664000-30668200	Strong transcription	Brain Substantia Nigra	brain
27	chr16:30664000-30668200	Strong transcription	Fetal Intestine Small	intestine
28	chr16:30664000-30668200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr16:30664000-30668200	Weak transcription	Stomach Mucosa	stomach
30	chr16:30664000-30668200	Strong transcription	NHEK	skin
31	chr16:30664000-30668400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr16:30664000-30668400	Strong transcription	HSMM	muscle
33	chr16:30664000-30668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr16:30664000-30669200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:30664200-30666600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr16:30664200-30666600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:30664200-30666600	Weak transcription	NHDF-Ad	bronchial
38	chr16:30664200-30667200	Strong transcription	Fetal Thymus	thymus
39	chr16:30664200-30667400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr16:30664200-30667400	Strong transcription	HUVEC	blood vessel
41	chr16:30664200-30667800	Strong transcription	Right Ventricle	heart
42	chr16:30664200-30667800	Strong transcription	HepG2	liver
43	chr16:30664200-30668000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr16:30664200-30668000	Strong transcription	Adipose Nuclei	Adipose
45	chr16:30664200-30668000	Strong transcription	Liver	Liver
46	chr16:30664200-30668000	Strong transcription	Brain Angular Gyrus	brain
47	chr16:30664200-30668000	Strong transcription	Placenta	Placenta
48	chr16:30664200-30668000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:30664200-30668200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:30664200-30668200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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