Variant report

Variant	rs8048078
Chromosome Location	chr16:70737106-70737107
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	MXI1	chr16:70736779-70738925	IMR90	lung:	n/a	chr16:70738160-70738169
2	POLR2A	chr16:70736780-70737839	U87	brain:	n/a	n/a
3	POLR2A	chr16:70736882-70737753	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr16:70737020-70737170	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr16:70736841-70737734	IMR90	lung:	n/a	chr16:70737601-70737611 chr16:70737016-70737028
6	MAX	chr16:70736874-70737444	SK-N-SH	brain:	n/a	chr16:70737373-70737382 chr16:70737385-70737395
7	MAX	chr16:70737062-70737235	HepG2	liver:	n/a	n/a
8	TEAD4	chr16:70736935-70737358	H1-hESC	embryonic stem cell:	n/a	chr16:70737198-70737207
9	MAFK	chr16:70736822-70737610	IMR90	lung:	n/a	chr16:70737371-70737380 chr16:70737390-70737405 chr16:70737373-70737383 chr16:70737037-70737051
10	POLR2A	chr16:70736874-70737863	IMR90	lung:	n/a	n/a
11	CEBPB	chr16:70736952-70737572	IMR90	lung:	n/a	n/a
12	MXI1	chr16:70736764-70739094	SK-N-SH	brain:	n/a	chr16:70739035-70739044 chr16:70738160-70738169
13	TEAD4	chr16:70736941-70737429	ECC-1	luminal epithelium:	n/a	chr16:70737198-70737207
14	MAX	chr16:70736885-70737371	ECC-1	luminal epithelium:	n/a	n/a
15	MAFK	chr16:70736946-70737205	HepG2	liver:	n/a	chr16:70737037-70737051
16	MAFF	chr16:70736890-70737183	HepG2	liver:	n/a	chr16:70737038-70737056
17	CTCF	chr16:70736980-70737130	AG04449	skin:	n/a	chr16:70736982-70736991
18	POLR2A	chr16:70736885-70737839	U87	brain:	n/a	n/a
19	MAFK	chr16:70736973-70737162	HepG2	liver:	n/a	chr16:70737037-70737051
20	POLR2A	chr16:70736984-70737886	U87	brain:	n/a	n/a
21	RAD21	chr16:70736651-70738709	SK-N-SH	brain:	n/a	chr16:70737601-70737611 chr16:70737016-70737028
22	MAX	chr16:70736914-70737823	ECC-1	luminal epithelium:	n/a	chr16:70737373-70737382 chr16:70737385-70737395
23	MAX	chr16:70736897-70737856	SK-N-SH	brain:	n/a	chr16:70737373-70737382 chr16:70737385-70737395
24	MAZ	chr16:70735036-70739510	IMR90	lung:	n/a	chr16:70737373-70737382 chr16:70738160-70738171 chr16:70739028-70739038 chr16:70737385-70737395
25	CTCF	chr16:70736963-70737806	IMR90	lung:	n/a	chr16:70737700-70737713 chr16:70737700-70737713 chr16:70736982-70736991 chr16:70737468-70737477
26	POLR2A	chr16:70736927-70737133	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70718149..70722046-chr16:70735012..70737866,4	K562	blood:
2	chr16:70729613..70734171-chr16:70734566..70738930,4	K562	blood:
3	chr16:70737004..70737719-chr16:70772011..70772709,2	MCF-7	breast:
4	chr16:70736848..70738799-chr16:70767007..70768655,2	MCF-7	breast:
5	chr16:70735575..70742322-chr16:70778614..70782532,8	MCF-7	breast:
6	chr16:70734375..70737351-chr16:70807793..70809854,2	K562	blood:
7	chr16:70735376..70737642-chr16:70737721..70740521,2	K562	blood:
8	chr16:70703850..70706247-chr16:70735267..70737927,2	MCF-7	breast:

Variant related genes	Relation type
VAC14	TF binding region
ENSG00000103043	Chromatin interaction
ENSG00000260156	Chromatin interaction
ENSG00000132613	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11640251	0.82[GIH][hapmap];0.87[JPT][hapmap]
rs11642770	0.87[GIH][hapmap];0.87[JPT][hapmap]
rs11642775	0.87[GIH][hapmap];0.87[JPT][hapmap]
rs11649305	0.87[JPT][hapmap]
rs2242126	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278984	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3785426	0.91[ASN][1000 genomes]
rs3813908	0.83[MEX][hapmap]
rs4985563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8054653	0.87[JPT][hapmap]
rs8059238	0.94[ASW][hapmap];0.87[JPT][hapmap]
rs936301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9673700	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9934869	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906874	chr16:70677785-70740707	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906875	chr16:70677785-70742536	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv572946	chr16:70694000-70740707	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv471094	chr16:70694000-70749970	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv906885	chr16:70696367-70742536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1059226	chr16:70708698-70779144	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
15	nsv906888	chr16:70716742-70742536	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8048078	EDC4	cis	cerebellum	SCAN
rs8048078	IL34	cis	parietal	SCAN
rs8048078	TMED6	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70720400-70753200	Weak transcription	Primary B cells from cord blood	blood
2	chr16:70727000-70770800	Weak transcription	GM12878-XiMat	blood
3	chr16:70728800-70738600	Enhancers	Fetal Heart	heart
4	chr16:70729800-70737200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:70730600-70737800	Weak transcription	Hela-S3	cervix
6	chr16:70730600-70738800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr16:70731400-70755000	Weak transcription	Small Intestine	intestine
8	chr16:70732000-70740600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr16:70732000-70746600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:70732200-70740800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr16:70732800-70737800	Weak transcription	Pancreas	Pancrea
12	chr16:70732800-70741000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:70732800-70744400	Enhancers	Fetal Muscle Trunk	muscle
14	chr16:70732800-70745000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr16:70732800-70749600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:70733000-70738200	Enhancers	Brain Anterior Caudate	brain
17	chr16:70733200-70737200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr16:70733200-70737600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:70733200-70738600	Enhancers	Brain Hippocampus Middle	brain
20	chr16:70733200-70739400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:70733200-70759400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr16:70733400-70737200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:70733400-70738600	Enhancers	Brain Cingulate Gyrus	brain
24	chr16:70733400-70738800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:70733400-70739200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:70733400-70741000	Genic enhancers	Fetal Stomach	stomach
27	chr16:70733400-70742400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr16:70733400-70743600	Enhancers	Placenta	Placenta
29	chr16:70733400-70754000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:70733600-70737800	Enhancers	NHDF-Ad	bronchial
31	chr16:70733600-70738200	Enhancers	Brain Substantia Nigra	brain
32	chr16:70733600-70738200	Enhancers	Right Atrium	heart
33	chr16:70733600-70738400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:70733600-70739400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr16:70733600-70739800	Enhancers	Fetal Muscle Leg	muscle
36	chr16:70733600-70742400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr16:70733800-70737600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr16:70733800-70738400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr16:70733800-70738400	Enhancers	Left Ventricle	heart
40	chr16:70733800-70738600	Enhancers	Right Ventricle	heart
41	chr16:70733800-70739600	Enhancers	NH-A	brain
42	chr16:70733800-70742000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr16:70733800-70743400	Enhancers	Fetal Thymus	thymus
44	chr16:70733800-70744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:70733800-70753400	Weak transcription	Dnd41	blood
46	chr16:70734000-70738000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr16:70734000-70738600	Enhancers	Brain Germinal Matrix	brain
48	chr16:70734000-70739000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr16:70734000-70740600	Weak transcription	Gastric	stomach
50	chr16:70734000-70741800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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