Variant report

Variant	rs3784929
Chromosome Location	chr16:75677027-75677028
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	chr16:75676950-75677034	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75602005..75604568-chr16:75676521..75678047,2	MCF-7	breast:
2	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:
3	chr16:75676829..75679257-chr16:75786783..75789607,2	MCF-7	breast:

Variant related genes	Relation type
TERF2IP	TF binding region
KARS	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11149842	1.00[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11149843	0.87[GIH][hapmap]
rs11643215	0.90[CEU][hapmap]
rs12595883	0.82[JPT][hapmap]
rs12596033	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12596857	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12598094	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12598741	0.82[JPT][hapmap]
rs12599322	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12600271	0.87[JPT][hapmap]
rs16940253	0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs16940467	0.93[JPT][hapmap]
rs16941533	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17697211	0.81[ASN][1000 genomes]
rs17764821	0.87[JPT][hapmap]
rs1865493	0.90[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1979717	0.87[JPT][hapmap];0.84[MEX][hapmap]
rs2082751	0.91[AMR][1000 genomes]
rs2164245	0.87[JPT][hapmap]
rs2242406	0.84[MEX][hapmap]
rs2289063	0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2550904	0.80[JPT][hapmap]
rs2738792	0.81[AMR][1000 genomes]
rs2903106	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736377	0.80[MEX][hapmap]
rs3743598	0.84[MEX][hapmap]
rs3743599	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs3743603	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs3851741	0.84[MEX][hapmap]
rs41505349	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888440	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4888441	0.84[CHB][hapmap]
rs4888442	0.80[ASN][1000 genomes]
rs5010692	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57396453	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7186966	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7193066	0.80[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs8051241	0.81[ASN][1000 genomes]
rs8060972	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8061505	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs963820	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9934159	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3784929	ADAT1	cis	cerebellum	SCAN
rs3784929	ST3GAL2	cis	cerebellum	SCAN
rs3784929	ZNRF1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:75659000-75678200	Strong transcription	Fetal Muscle Leg	muscle
7	chr16:75659000-75678400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr16:75659200-75678000	Strong transcription	HepG2	liver
9	chr16:75659200-75680000	Strong transcription	Fetal Stomach	stomach
10	chr16:75659200-75680000	Strong transcription	A549	lung
11	chr16:75659200-75680600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:75659400-75677200	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr16:75659400-75678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr16:75659400-75678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr16:75659400-75679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:75659400-75680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:75659600-75678200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr16:75659600-75678200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr16:75659600-75678200	Strong transcription	Fetal Intestine Large	intestine
20	chr16:75659600-75678400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:75659600-75678600	Strong transcription	Liver	Liver
22	chr16:75659600-75678800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr16:75659600-75679200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr16:75659600-75679400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:75659600-75679600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:75659600-75679600	Strong transcription	Placenta	Placenta
27	chr16:75659600-75679600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr16:75659600-75679800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr16:75659600-75679800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr16:75659800-75677400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:75659800-75678600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:75659800-75679400	Strong transcription	HSMM	muscle
33	chr16:75659800-75679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr16:75659800-75679600	Strong transcription	Osteobl	bone
35	chr16:75660000-75677200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr16:75660000-75678200	Strong transcription	Fetal Intestine Small	intestine
37	chr16:75660000-75679000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr16:75660000-75679600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr16:75661000-75678200	Strong transcription	Colon Smooth Muscle	Colon
40	chr16:75662600-75677800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr16:75662800-75677400	Strong transcription	Adipose Nuclei	Adipose
42	chr16:75662800-75677400	Strong transcription	Dnd41	blood
43	chr16:75662800-75678200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr16:75662800-75678200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr16:75663000-75677600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr16:75663000-75678600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr16:75663200-75677800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr16:75663200-75679200	Strong transcription	Fetal Thymus	thymus
49	chr16:75663400-75678400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr16:75663400-75678600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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