Variant report

Variant	rs1060962
Chromosome Location	chr3:49708502-49708503
allele	G/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	chr3:49708470-49708614	A549	lung:	n/a	n/a
2	POLR2A	chr3:49707857-49708566	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:49707409-49708672	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr3:49708134-49708644	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:49707209-49709609	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49707849-49708666	HCT-116	colon:	n/a	n/a
7	CTCF	chr3:49708228-49709922	SK-N-SH	brain:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
8	POLR2A	chr3:49706418-49708747	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:49708455-49708511	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:49707577-49708713	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr3:49707981-49708690	HCT-116	colon:	n/a	n/a
12	POLR2A	chr3:49708500-49708525	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr3:49708485-49709629	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:49706366-49708956	K562	blood:	n/a	n/a
15	POLR2A	chr3:49708052-49708647	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:49708450-49708619	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:49708332-49708958	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:49707310-49708795	Raji	blood:	n/a	n/a
19	POLR2A	chr3:49707334-49709533	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49573379..49575748-chr3:49707460..49709611,2	MCF-7	breast:
2	chr3:49575867..49578786-chr3:49708422..49711347,4	K562	blood:
3	chr3:49591498..49593888-chr3:49707123..49708705,2	K562	blood:
4	chr3:49588369..49592998-chr3:49704328..49708705,5	K562	blood:
5	chr3:49609338..49612017-chr3:49707292..49709835,2	K562	blood:
6	chr3:49603620..49605380-chr3:49707989..49710873,2	MCF-7	breast:
7	chr3:49576201..49578760-chr3:49706386..49709294,3	MCF-7	breast:
8	chr3:49507427..49510910-chr3:49706254..49709319,3	MCF-7	breast:

Variant related genes	Relation type
APEH	TF binding region
ENSG00000164061	Chromatin interaction
ENSG00000226913	Chromatin interaction
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1050088	0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs11130199	0.86[CHD][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap]
rs11130212	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130213	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1131095	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs11709525	0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs11710037	0.81[ASN][1000 genomes]
rs11718165	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11919311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12490267	0.87[EUR][1000 genomes]
rs12497288	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13316695	0.81[ASN][1000 genomes]
rs1352890	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1568661	0.86[CHD][hapmap];0.94[GIH][hapmap]
rs1801143	0.85[GIH][hapmap]
rs1826347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1873625	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs1873626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172252	0.81[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960548	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3197999	0.92[CHD][hapmap];0.83[GIH][hapmap]
rs34762726	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs35007338	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35404120	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35701831	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs3811697	0.85[GIH][hapmap]
rs3870338	0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs3924462	0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap]
rs4283605	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs4625	0.85[GIH][hapmap]
rs4855835	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4855847	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855859	0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap]
rs4855864	0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855883	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855884	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766131	0.85[GIH][hapmap]
rs6767878	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6770670	0.81[ASN][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs6803222	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs7622302	0.85[GIH][hapmap]
rs7637999	0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap]
rs9812791	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs9822268	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs9823546	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9824092	0.81[ASN][1000 genomes]
rs9827708	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs9836291	0.91[ASN][1000 genomes]
rs9837027	0.85[GIH][hapmap]
rs9853683	0.85[GIH][hapmap]
rs9858213	1.00[JPT][hapmap]
rs9858280	0.85[GIH][hapmap]
rs9858542	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9862080	0.81[ASN][1000 genomes]
rs9875617	0.85[GIH][hapmap]
rs9882740	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1060962	WDR6	cis	lymphoblastoid	seeQTL
rs1060962	CCDC71	cis	cerebellum	SCAN
rs1060962	ARIH2	cis	parietal	SCAN
rs1060962	ALS2CL	cis	cerebellum	SCAN
rs1060962	IP6K2	cis	cerebellum	SCAN
rs1060962	CISH	cis	lymphoblastoid	seeQTL
rs1060962	CELSR3	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
2	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
6	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
9	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
10	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
11	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
12	chr3:49703800-49710600	Enhancers	Liver	Liver
13	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:49704200-49710600	Weak transcription	Gastric	stomach
15	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:49704600-49709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:49704800-49710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:49705000-49710600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:49705400-49709000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:49705600-49710600	Weak transcription	Brain Anterior Caudate	brain
24	chr3:49705600-49710600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:49705600-49710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:49705800-49709000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:49706000-49709000	Weak transcription	Thymus	Thymus
28	chr3:49706000-49710600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:49706200-49708600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:49706200-49708800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:49706200-49710600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:49706200-49710600	Weak transcription	Brain Angular Gyrus	brain
33	chr3:49706200-49710600	Weak transcription	Fetal Intestine Large	intestine
34	chr3:49706200-49710600	Weak transcription	Fetal Intestine Small	intestine
35	chr3:49706400-49709000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:49706400-49709000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:49706800-49709600	Weak transcription	Fetal Kidney	kidney
38	chr3:49706800-49710600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:49706800-49710600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:49706800-49710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:49706800-49710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:49706800-49710600	Weak transcription	Stomach Mucosa	stomach
43	chr3:49707000-49709400	Weak transcription	Hela-S3	cervix
44	chr3:49707000-49710600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:49707000-49710600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:49707000-49710600	Weak transcription	Adipose Nuclei	Adipose
47	chr3:49707000-49710600	Weak transcription	Esophagus	oesophagus
48	chr3:49707000-49710600	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:49707000-49710600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:49707000-49710600	Weak transcription	HSMM	muscle

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