Variant report

Variant	rs2286651
Chromosome Location	chr3:48694147-48694148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48616186..48618444-chr3:48693740..48696673,2	MCF-7	breast:
2	chr3:48671879..48673850-chr3:48694137..48695935,2	MCF-7	breast:
3	chr3:48682961..48685623-chr3:48693830..48696752,2	MCF-7	breast:
4	chr3:48689444..48692588-chr3:48693029..48695522,3	MCF-7	breast:
5	chr3:48631571..48635730-chr3:48691196..48694379,3	K562	blood:

Variant related genes	Relation type
ENSG00000114270	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000211535	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11557629	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706203	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11706983	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11708786	0.80[AMR][1000 genomes]
rs11715177	0.80[AMR][1000 genomes]
rs11719291	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12107252	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12107418	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13063223	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13063312	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13076269	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13086240	0.82[AMR][1000 genomes]
rs13090013	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13096357	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316551	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13324119	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13324142	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13324950	0.80[AMR][1000 genomes]
rs13434258	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17080319	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2276850	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276852	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2310996	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2310997	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452701	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28567949	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28657585	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28793701	0.80[AMR][1000 genomes]
rs34096717	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34153629	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34368826	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34638686	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35064573	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3733086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806694	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821876	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077495	0.80[AMR][1000 genomes]
rs56735597	0.80[AMR][1000 genomes]
rs57334642	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768448	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773261	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68042649	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73078349	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73078362	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs740787	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620853	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631574	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809222	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9811027	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9811318	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812200	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812977	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9821797	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9834996	0.80[AMR][1000 genomes]
rs9836462	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841602	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9854034	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9868809	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9873726	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9877542	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9877685	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9878063	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882549	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	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
9	esv3407141	chr3:48692473-48695321	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2286651	WDR6	cis	Adipose Subcutaneous	GTEx
rs2286651	SLC26A6	cis	lung	GTEx
rs2286651	WDR6	cis	Esophagus Mucosa	GTEx
rs2286651	WDR6	cis	Whole Blood	GTEx
rs2286651	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48674800-48695600	Weak transcription	Hela-S3	cervix
2	chr3:48675000-48694200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:48675000-48697200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48680000-48695400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:48693000-48694200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:48693000-48694400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:48693000-48694400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:48693000-48694400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:48693000-48694400	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:48693000-48694400	Active TSS	Brain Hippocampus Middle	brain
11	chr3:48693000-48694400	Active TSS	Colon Smooth Muscle	Colon
12	chr3:48693000-48694400	Active TSS	Osteobl	bone
13	chr3:48693000-48694800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:48693200-48694200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:48693200-48694200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:48693200-48694200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:48693200-48694200	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr3:48693200-48694200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:48693200-48694200	Active TSS	Fetal Intestine Small	intestine
20	chr3:48693200-48694200	Active TSS	Ovary	ovary
21	chr3:48693200-48694200	Active TSS	Right Atrium	heart
22	chr3:48693200-48694200	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:48693200-48694400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr3:48693200-48694400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:48693200-48694400	Active TSS	Brain Angular Gyrus	brain
26	chr3:48693200-48694400	Active TSS	Brain Anterior Caudate	brain
27	chr3:48693200-48694400	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:48693200-48694600	Active TSS	Primary T cells from cord blood	blood
29	chr3:48693200-48694600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:48693200-48694600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:48693200-48694600	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:48693200-48694800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr3:48693200-48695600	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
34	chr3:48693400-48694200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:48693400-48694200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:48693400-48694200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:48693400-48694200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:48693400-48694200	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:48693400-48694200	Active TSS	Thymus	Thymus
40	chr3:48693400-48694400	Active TSS	Psoas Muscle	Psoas
41	chr3:48693400-48694400	Active TSS	HSMM	muscle
42	chr3:48693400-48694600	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:48693400-48694600	Flanking Active TSS	Lung	lung
44	chr3:48693400-48694600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:48693400-48696800	Enhancers	Fetal Brain Male	brain
46	chr3:48693600-48694200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:48693600-48694200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:48693600-48694200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:48693600-48694200	Active TSS	Liver	Liver
50	chr3:48693600-48694200	Active TSS	Gastric	stomach

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