Variant report

Variant	rs34638686
Chromosome Location	chr3:48682658-48682659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:48682600-48682662	Fibrobl	skin:	n/a	n/a
2	POLR2A	chr3:48682436-48682694	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48682486-48682847	U87	brain:	n/a	n/a
4	POLR2A	chr3:48682151-48682900	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:48682558-48682706	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:48682396-48682820	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr3:48682469-48682706	MCF-7	breast:	n/a	n/a
8	CTCF	chr3:48682560-48682710	NHEK	skin:	n/a	n/a
9	POLR2A	chr3:48682478-48682679	H1-hESC	embryonic stem cell:	n/a	n/a
10	NR2F2	chr3:48682512-48683009	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48672218..48676276-chr3:48681744..48684304,3	MCF-7	breast:
2	chr3:48682002..48685368-chr3:48687260..48690560,5	K562	blood:
3	chr3:48678696..48680321-chr3:48682057..48684957,2	K562	blood:
4	chr3:48680392..48682297-chr3:48682436..48685130,3	K562	blood:
5	chr3:48672326..48679145-chr3:48682119..48686391,6	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4793	TF binding region
CELSR3	TF binding region
ENSG00000263898	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12107252	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12107418	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12715429	0.84[EUR][1000 genomes]
rs13063312	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13070798	0.84[EUR][1000 genomes]
rs13076269	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13096357	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13324119	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13324142	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276850	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276852	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286651	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286652	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2302295	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2310996	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2310997	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28452701	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34096717	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34368826	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34577723	0.80[AMR][1000 genomes]
rs3733086	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806694	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821875	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821876	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57334642	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768448	0.80[EUR][1000 genomes]
rs6773261	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792156	0.81[ASN][1000 genomes]
rs68042649	0.80[EUR][1000 genomes]
rs740787	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620853	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7631574	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809222	0.80[EUR][1000 genomes]
rs9811318	0.80[EUR][1000 genomes]
rs9812200	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821797	0.80[EUR][1000 genomes]
rs9836462	0.80[EUR][1000 genomes]
rs9841602	0.80[EUR][1000 genomes]
rs9868809	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873726	0.80[EUR][1000 genomes]
rs9878063	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers 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 miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS 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	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs34638686	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs34638686	SLC26A6	cis	Muscle Skeletal	GTEx
rs34638686	WDR6	cis	lung	GTEx
rs34638686	WDR6	cis	Esophagus Mucosa	GTEx
rs34638686	TMEM89	cis	Artery Tibial	GTEx
rs34638686	SLC26A6	cis	lung	GTEx
rs34638686	WDR6	cis	Adipose Subcutaneous	GTEx
rs34638686	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48673600-48693400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:48673800-48692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:48674000-48683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:48674000-48692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:48674000-48693400	Weak transcription	Fetal Brain Male	brain
6	chr3:48674000-48693600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:48674200-48692600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:48674400-48685800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:48674400-48691000	Weak transcription	Spleen	Spleen
10	chr3:48674400-48692800	Weak transcription	Placenta	Placenta
11	chr3:48674400-48692800	Weak transcription	Right Ventricle	heart
12	chr3:48674400-48693600	Weak transcription	Gastric	stomach
13	chr3:48674800-48692600	Strong transcription	Fetal Brain Female	brain
14	chr3:48674800-48695600	Weak transcription	Hela-S3	cervix
15	chr3:48675000-48689200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:48675000-48693600	Weak transcription	A549	lung
17	chr3:48675000-48694200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:48675000-48697200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:48675200-48687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:48675200-48692400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:48675400-48686200	Weak transcription	HepG2	liver
22	chr3:48676400-48684600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr3:48676400-48687400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:48676400-48689200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:48676600-48684400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:48676600-48684400	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr3:48676600-48687200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:48676600-48687200	Strong transcription	Brain Angular Gyrus	brain
29	chr3:48676600-48691800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:48676800-48684600	Strong transcription	Brain Anterior Caudate	brain
31	chr3:48676800-48684600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr3:48677000-48687200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:48677400-48686000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:48677600-48692200	Strong transcription	Brain Germinal Matrix	brain
35	chr3:48678400-48682800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:48678400-48683800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:48678400-48684400	Strong transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:48678600-48684000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48678800-48684600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:48679600-48684400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:48680000-48695400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:48680200-48684000	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:48680800-48690600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:48681000-48690600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:48681200-48683400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:48681600-48685400	Weak transcription	Fetal Intestine Small	intestine
47	chr3:48681800-48684400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:48682200-48684400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:48682200-48684400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:48682200-48684600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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