Variant report

Variant	rs1352420
Chromosome Location	chr3:48757291-48757292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48754698..48757669-chr3:48775875..48778896,4	K562	blood:
2	chr3:48755633..48757669-chr3:48777396..48780297,2	K562	blood:
3	chr3:48754717..48757980-chr3:48775781..48778989,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10780033	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs10865952	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130176	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs11557629	0.90[ASN][1000 genomes]
rs11705888	0.83[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]
rs11715689	0.82[ASN][1000 genomes]
rs11719291	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11920534	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11924597	0.92[CEU][hapmap]
rs11928552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs12107418	0.86[YRI][hapmap]
rs12493289	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12493578	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]
rs12497850	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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]
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];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs4077495	0.95[ASN][1000 genomes]
rs4858798	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858828	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858831	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974079	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs4974085	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs4974087	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs61137521	0.81[ASN][1000 genomes]
rs6442130	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446252	0.92[CEU][hapmap]
rs6446253	0.92[CEU][hapmap]
rs6788650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6791542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792510	0.82[EUR][1000 genomes]
rs7373778	0.81[EUR][1000 genomes]
rs7430501	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs7431710	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs7431857	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs7616815	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7623023	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs7627404	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7630742	0.84[EUR][1000 genomes]
rs7633840	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7647813	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs7649458	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap]
rs9311430	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs9311432	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9311433	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9311434	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs9682444	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs9755490	0.92[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs9811027	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9811318	0.83[ASW][hapmap];0.93[YRI][hapmap]
rs9834996	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9835307	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs9836462	0.83[YRI][hapmap]
rs9841602	0.83[YRI][hapmap]
rs9848203	0.87[ASN][1000 genomes]
rs9850134	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs9854034	0.92[ASN][1000 genomes]
rs9873726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9876848	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
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]
rs9884022	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:35)

SNP	Gene	Cis/trans	Tissue	Source
rs1352420	WDR6	cis	Muscle Skeletal	GTEx
rs1352420	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs1352420	WDR6	cis	uninvolved skin	skin_eQTL
rs1352420	WDR6	cis	Artery Tibial	GTEx
rs1352420	WDR6	cis	cerebellum	SCAN
rs1352420	DALRD3	cis	parietal	SCAN
rs1352420	AMT	cis	parietal	SCAN
rs1352420	WDR6	cis	lung	GTEx
rs1352420	CCDC36	cis	Artery Tibial	GTEx
rs1352420	WDR6	cis	parietal	SCAN
rs1352420	WDR6	cis	Adipose Subcutaneous	GTEx
rs1352420	WDR6	cis	Nerve Tibial	GTEx
rs1352420	WDR6	cis	Esophagus Mucosa	GTEx
rs1352420	NCKIPSD	cis	Muscle Skeletal	GTEx
rs1352420	CCDC71	cis	cerebellum	SCAN
rs1352420	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs1352420	AMT	cis	Thyroid	GTEx
rs1352420	ZNF589	cis	parietal	SCAN
rs1352420	NCKIPSD	cis	Whole Blood	GTEx
rs1352420	C3orf62	cis	cerebellum	SCAN
rs1352420	NCKIPSD	cis	cerebellum	SCAN
rs1352420	WDR6	cis	lymphoblastoid	seeQTL
rs1352420	NICN1	cis	Thyroid	GTEx
rs1352420	AMT	cis	cerebellum	SCAN
rs1352420	NCKIPSD	cis	parietal	SCAN
rs1352420	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs1352420	NCKIPSD	cis	lung	GTEx
rs1352420	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs1352420	DALRD3	cis	cerebellum	SCAN
rs1352420	NCKIPSD	cis	Nerve Tibial	GTEx
rs1352420	NICN1-AS1	cis	Thyroid	GTEx
rs1352420	P4HTM	cis	parietal	SCAN
rs1352420	WDR6	cis	Whole Blood	GTEx
rs1352420	TLR9	cis	parietal	SCAN
rs1352420	ZNF589	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48754800-48759000	Weak transcription	Gastric	stomach
2	chr3:48755200-48757600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:48755200-48758000	Weak transcription	Fetal Lung	lung
4	chr3:48755200-48759000	Weak transcription	Fetal Kidney	kidney
5	chr3:48755200-48760000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:48755200-48760200	Weak transcription	Small Intestine	intestine
7	chr3:48755400-48757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:48755400-48757600	Weak transcription	Spleen	Spleen
9	chr3:48755400-48758000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:48755400-48758000	Weak transcription	Stomach Mucosa	stomach
11	chr3:48755400-48759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:48755400-48760200	Weak transcription	Colonic Mucosa	Colon
13	chr3:48755400-48760200	Weak transcription	A549	lung
14	chr3:48755400-48760400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:48755600-48760200	Weak transcription	K562	blood
16	chr3:48756000-48759000	Weak transcription	Pancreas	Pancrea
17	chr3:48756200-48758800	Weak transcription	HepG2	liver
18	chr3:48756800-48758800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:48757000-48757600	Weak transcription	Fetal Intestine Small	intestine
20	chr3:48757000-48760000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:48757200-48757400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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