Variant report

Variant	rs12493578
Chromosome Location	chr3:48730116-48730117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48708844..48711305-chr3:48727090..48731325,3	K562	blood:
2	chr3:48730035..48731678-chr3:48732538..48734765,2	MCF-7	breast:
3	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
4	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:

Variant related genes	Relation type
ENSG00000271973	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10780033	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs10865952	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130176	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs11557629	1.00[ASN][1000 genomes]
rs11705888	0.81[EUR][1000 genomes]
rs11706203	0.95[ASN][1000 genomes]
rs11706983	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11708786	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11713694	1.00[CHD][hapmap]
rs11715177	0.95[ASN][1000 genomes]
rs11719291	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11928552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs12493289	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12497850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063223	0.95[ASN][1000 genomes]
rs13090013	0.95[ASN][1000 genomes]
rs13316551	0.95[ASN][1000 genomes]
rs13324950	0.95[ASN][1000 genomes]
rs13434258	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1352420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17080319	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28567949	0.95[ASN][1000 genomes]
rs28657585	0.95[ASN][1000 genomes]
rs28793701	0.95[ASN][1000 genomes]
rs34037363	1.00[CHD][hapmap]
rs34153629	0.95[ASN][1000 genomes]
rs34577723	0.87[ASN][1000 genomes]
rs35064573	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3774628	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs4077495	0.95[ASN][1000 genomes]
rs4858798	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858828	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858831	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974079	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4974085	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4974087	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs61137521	0.81[ASN][1000 genomes]
rs6442130	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6446252	0.92[CEU][hapmap]
rs6446253	0.92[CEU][hapmap]
rs6788650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6792510	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7430501	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs7431857	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs7616815	0.92[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7623023	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7627404	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs7630742	0.81[EUR][1000 genomes]
rs7633840	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7647813	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs7649458	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap]
rs9311430	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs9311432	0.90[CEU][hapmap]
rs9311433	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9311434	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9682444	0.92[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9755490	0.92[CEU][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs9811027	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9811318	0.86[YRI][hapmap]
rs9834996	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9835307	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9848203	0.87[ASN][1000 genomes]
rs9854034	0.92[ASN][1000 genomes]
rs9873726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9876848	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs9877542	0.95[ASN][1000 genomes]
rs9877685	0.95[ASN][1000 genomes]
rs9882549	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[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	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
2	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
3	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
4	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

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs12493578	WDR6	cis	Nerve Tibial	GTEx
rs12493578	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs12493578	TLR9	cis	parietal	SCAN
rs12493578	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12493578	WDR6	cis	parietal	SCAN
rs12493578	WDR6	cis	lymphoblastoid	seeQTL
rs12493578	NCKIPSD	cis	Nerve Tibial	GTEx
rs12493578	WDR6	cis	Artery Tibial	GTEx
rs12493578	WDR6	cis	Adipose Subcutaneous	GTEx
rs12493578	NCKIPSD	cis	multi-tissue	Pritchard
rs12493578	WDR6	cis	cerebellum	SCAN
rs12493578	NCKIPSD	cis	Whole Blood	GTEx
rs12493578	ZNF589	cis	cerebellum	SCAN
rs12493578	NICN1	cis	multi-tissue	Pritchard
rs12493578	AMT	cis	Thyroid	GTEx
rs12493578	WDR6	cis	uninvolved skin	skin_eQTL
rs12493578	AMT	cis	multi-tissue	Pritchard
rs12493578	P4HTM	cis	parietal	SCAN
rs12493578	WDR6	cis	Whole Blood	GTEx
rs12493578	C3orf62	cis	cerebellum	SCAN
rs12493578	WDR6	cis	Muscle Skeletal	GTEx
rs12493578	NICN1	cis	Thyroid	GTEx
rs12493578	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12493578	DALRD3	cis	parietal	SCAN
rs12493578	NCKIPSD	cis	Muscle Skeletal	GTEx
rs12493578	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12493578	NCKIPSD	cis	cerebellum	SCAN
rs12493578	WDR6	cis	Esophagus Mucosa	GTEx
rs12493578	CCDC36	cis	Artery Tibial	GTEx
rs12493578	NCKIPSD	cis	parietal	SCAN
rs12493578	AMT	cis	cerebellum	SCAN
rs12493578	WDR6	cis	multi-tissue	Pritchard
rs12493578	NICN1-AS1	cis	Thyroid	GTEx
rs12493578	ZNF589	cis	parietal	SCAN
rs12493578	AMT	cis	parietal	SCAN
rs12493578	DALRD3	cis	cerebellum	SCAN
rs12493578	WDR6	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:48724200-48730200	Weak transcription	K562	blood
4	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:48724400-48730400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
8	chr3:48724600-48730600	Strong transcription	Fetal Brain Female	brain
9	chr3:48724600-48731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:48724600-48731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:48724600-48732000	Strong transcription	Fetal Lung	lung
12	chr3:48724600-48732200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:48724600-48732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:48724600-48732400	Strong transcription	Fetal Intestine Large	intestine
15	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
16	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
19	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
21	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
22	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:48724800-48730200	Weak transcription	Right Atrium	heart
24	chr3:48724800-48730200	Strong transcription	HSMMtube	muscle
25	chr3:48724800-48730800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:48724800-48731000	Strong transcription	Adipose Nuclei	Adipose
27	chr3:48724800-48731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:48724800-48731200	Strong transcription	Fetal Kidney	kidney
29	chr3:48724800-48731200	Strong transcription	HUVEC	blood vessel
30	chr3:48724800-48731400	Strong transcription	Aorta	Aorta
31	chr3:48724800-48731600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:48724800-48731600	Strong transcription	Hela-S3	cervix
33	chr3:48724800-48732000	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr3:48724800-48732200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:48724800-48732200	Strong transcription	Pancreas	Pancrea
36	chr3:48724800-48732400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr3:48724800-48732400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:48724800-48732400	Strong transcription	Colonic Mucosa	Colon
39	chr3:48724800-48732400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr3:48724800-48732400	Strong transcription	Fetal Intestine Small	intestine
41	chr3:48724800-48732400	Strong transcription	Gastric	stomach
42	chr3:48724800-48732400	Strong transcription	Lung	lung
43	chr3:48724800-48732600	Strong transcription	Spleen	Spleen
44	chr3:48724800-48732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:48724800-48733000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:48724800-48733000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:48724800-48733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:48724800-48733800	Strong transcription	HepG2	liver
49	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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