Variant report

Variant	rs9814987
Chromosome Location	chr3:49207849-49207850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:49207720-49207870	GM12869	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49064349..49066955-chr3:49207317..49210098,3	MCF-7	breast:
2	chr3:49202977..49205406-chr3:49206821..49209199,3	MCF-7	breast:
3	chr3:49165567..49167426-chr3:49206030..49208250,2	K562	blood:
4	chr3:49202213..49205140-chr3:49207105..49209971,4	MCF-7	breast:
5	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
6	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:
7	chr3:49207496..49209154-chr3:49376769..49379124,2	MCF-7	breast:
8	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
9	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

No data

Variant related genes	Relation type
KLHDC8B	TF binding region
CCDC71	TF binding region
ENSG00000172037	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000270441	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10154895	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865954	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11130182	0.93[ASN][1000 genomes]
rs11130184	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710247	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11712006	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715581	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11716334	0.92[ASN][1000 genomes]
rs11716445	0.92[CEU][hapmap]
rs11716614	0.92[CEU][hapmap]
rs11718982	0.87[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719457	0.80[EUR][1000 genomes]
rs11720460	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11920267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487580	0.95[ASN][1000 genomes]
rs12490393	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12493001	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12629759	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12631989	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	0.95[ASN][1000 genomes]
rs12637576	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12715434	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13064784	0.90[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13072554	0.84[EUR][1000 genomes]
rs13077498	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13080725	0.82[EUR][1000 genomes]
rs13086240	0.80[EUR][1000 genomes]
rs13087930	0.80[EUR][1000 genomes]
rs13090839	0.80[EUR][1000 genomes]
rs13096406	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2117938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2304442	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap]
rs3212	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34326553	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34343820	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34504524	0.82[EUR][1000 genomes]
rs34509487	0.80[EUR][1000 genomes]
rs34566463	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34784192	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34889065	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34915642	0.88[MKK][hapmap]
rs35060561	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35102816	0.82[EUR][1000 genomes]
rs35108630	0.85[EUR][1000 genomes]
rs35174559	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36133651	0.80[ASN][1000 genomes]
rs3923475	0.83[EUR][1000 genomes]
rs4279134	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4308307	0.97[ASN][1000 genomes]
rs4499638	0.92[ASN][1000 genomes]
rs4513485	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4521268	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4536858	0.92[ASN][1000 genomes]
rs4955410	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4955418	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955420	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974080	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55713230	0.92[ASN][1000 genomes]
rs55921200	0.84[EUR][1000 genomes]
rs56306491	0.86[EUR][1000 genomes]
rs56318350	0.80[EUR][1000 genomes]
rs61583136	1.00[ASN][1000 genomes]
rs62262517	0.88[ASN][1000 genomes]
rs6414613	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446205	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67286839	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6770112	1.00[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6781790	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6784111	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6790914	0.92[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs71324939	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73084135	0.91[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap]
rs7615235	0.87[ASN][1000 genomes]
rs7621015	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7645551	0.82[ASN][1000 genomes]
rs7652746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9826525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9828310	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835439	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9846123	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9847839	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9855123	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9863142	0.88[MKK][hapmap]
rs9864406	0.91[MKK][hapmap]
rs9880088	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9814987	CCDC36	cis	cerebellum	SCAN
rs9814987	HEMK1	cis	parietal	SCAN
rs9814987	WDR6	cis	Esophagus Mucosa	GTEx
rs9814987	WDR6	cis	Adipose Subcutaneous	GTEx
rs9814987	WDR6	cis	parietal	SCAN
rs9814987	NICN1	cis	cerebellum	SCAN
rs9814987	WDR6	cis	Whole Blood	GTEx
rs9814987	ALAS1	cis	cerebellum	SCAN
rs9814987	WDR6	cis	Artery Tibial	GTEx
rs9814987	KBTBD3	trans	parietal	SCAN
rs9814987	ARIH2	cis	cerebellum	SCAN
rs9814987	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9814987	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9814987	RNF123	cis	parietal	SCAN
rs9814987	CSPG5	cis	parietal	SCAN
rs9814987	C3orf62	cis	cerebellum	SCAN
rs9814987	WDR6	cis	cerebellum	SCAN
rs9814987	LRRC2	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49204200-49208000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:49204200-49208000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:49204200-49208000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49204200-49208200	Weak transcription	HMEC	breast
5	chr3:49204400-49208000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49204400-49208000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:49204400-49208000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:49204400-49208000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:49204400-49208000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:49204400-49208000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:49204400-49208000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:49204400-49208000	Weak transcription	Adipose Nuclei	Adipose
13	chr3:49204400-49208000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:49204400-49208000	Weak transcription	NHDF-Ad	bronchial
15	chr3:49204400-49208000	Weak transcription	NHLF	lung
16	chr3:49204400-49208000	Weak transcription	Osteobl	bone
17	chr3:49204400-49208200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:49204400-49208200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:49204400-49208200	Weak transcription	Right Ventricle	heart
20	chr3:49204400-49208200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:49204400-49208200	Weak transcription	Small Intestine	intestine
22	chr3:49204400-49208200	Weak transcription	A549	lung
23	chr3:49204400-49208200	Weak transcription	HSMM	muscle
24	chr3:49204400-49208200	Weak transcription	HSMMtube	muscle
25	chr3:49204400-49208200	Weak transcription	NH-A	brain
26	chr3:49204400-49208200	Weak transcription	NHEK	skin
27	chr3:49204400-49208400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:49204400-49208400	Weak transcription	Left Ventricle	heart
29	chr3:49204400-49208400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:49204400-49208600	Weak transcription	Right Atrium	heart
31	chr3:49204600-49208000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:49204600-49208000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:49204600-49208000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:49204600-49208000	Weak transcription	Brain Anterior Caudate	brain
35	chr3:49204600-49208000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:49204600-49208000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:49204600-49208000	Weak transcription	Dnd41	blood
38	chr3:49204600-49208200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:49204600-49208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:49204600-49208200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:49204600-49208200	Weak transcription	Hela-S3	cervix
42	chr3:49204600-49208400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:49204600-49208400	Weak transcription	HUVEC	blood vessel
44	chr3:49204600-49208600	Weak transcription	Aorta	Aorta
45	chr3:49204800-49208000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:49204800-49208000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:49207200-49208200	Enhancers	Fetal Intestine Small	intestine
48	chr3:49207200-49208200	Enhancers	K562	blood
49	chr3:49207200-49208400	Enhancers	Fetal Thymus	thymus
50	chr3:49207400-49208000	Enhancers	HepG2	liver

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