Variant report

Variant	rs9837625
Chromosome Location	chr3:49215966-49215967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49210011..49212298-chr3:49215313..49217112,2	MCF-7	breast:
2	chr3:49136133..49137781-chr3:49215466..49218025,2	K562	blood:
3	chr3:49214354..49216613-chr3:49252087..49254601,2	K562	blood:
4	chr3:49131687..49134642-chr3:49213919..49216265,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC71-2	chr3:49215915-49215971	NONHSAT089681

Variant related genes	Relation type
ENSG00000172053	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000198218	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11130182	0.85[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713297	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11716334	0.89[ASN][1000 genomes]
rs11716445	0.92[CEU][hapmap]
rs11716614	0.92[CEU][hapmap]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.87[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12493001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	0.97[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12715434	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.87[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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34343820	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.81[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34784192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35060561	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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35102816	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4308307	0.90[ASN][1000 genomes]
rs4364202	0.85[ASN][1000 genomes]
rs4499638	0.95[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4536858	0.95[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955418	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974080	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];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55713230	0.95[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.92[ASN][1000 genomes]
rs62262517	0.85[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67286839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770112	0.92[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6790914	0.95[ASN][1000 genomes]
rs6794924	0.89[ASN][1000 genomes]
rs6795025	0.84[ASN][1000 genomes]
rs71324939	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.92[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap]
rs7615235	0.84[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814987	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]
rs9818758	0.82[YRI][hapmap]
rs9826525	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9828310	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848772	0.82[YRI][hapmap]
rs9850917	1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9855123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873994	0.82[YRI][hapmap]
rs9880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	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];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9837625	ARIH2	cis	cerebellum	SCAN
rs9837625	ALAS1	cis	cerebellum	SCAN
rs9837625	COL7A1	cis	parietal	SCAN
rs9837625	CCDC36	cis	cerebellum	SCAN
rs9837625	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9837625	C3orf62	cis	cerebellum	SCAN
rs9837625	WDR6	cis	Esophagus Mucosa	GTEx
rs9837625	WDR6	cis	Artery Tibial	GTEx
rs9837625	HEMK1	cis	parietal	SCAN
rs9837625	RNF123	cis	parietal	SCAN
rs9837625	CSPG5	cis	parietal	SCAN
rs9837625	NICN1	cis	cerebellum	SCAN
rs9837625	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9837625	WDR6	cis	parietal	SCAN
rs9837625	WDR6	cis	cerebellum	SCAN
rs9837625	WDR6	cis	Adipose Subcutaneous	GTEx
rs9837625	KBTBD3	trans	parietal	SCAN
rs9837625	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
2	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:49211400-49216000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:49211400-49217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49211800-49216000	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr3:49211800-49216200	Genic enhancers	Fetal Muscle Leg	muscle
7	chr3:49211800-49216600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:49212000-49216200	Weak transcription	Osteobl	bone
9	chr3:49212200-49218800	Weak transcription	HepG2	liver
10	chr3:49212600-49216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:49212800-49216200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:49212800-49217000	Strong transcription	Fetal Stomach	stomach
13	chr3:49213000-49217200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:49213400-49216000	Strong transcription	Fetal Intestine Small	intestine
15	chr3:49213400-49217600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49213400-49217800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:49213800-49216000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:49213800-49216000	Strong transcription	Ovary	ovary
19	chr3:49213800-49217200	Enhancers	Fetal Heart	heart
20	chr3:49213800-49217400	Weak transcription	Fetal Brain Female	brain
21	chr3:49214000-49216200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:49214000-49217400	Weak transcription	Gastric	stomach
23	chr3:49214000-49218000	Weak transcription	Brain Germinal Matrix	brain
24	chr3:49214000-49218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:49214000-49219200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:49214000-49221400	Weak transcription	Liver	Liver
27	chr3:49214000-49224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:49214200-49216000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:49214200-49216000	Weak transcription	Colonic Mucosa	Colon
30	chr3:49214200-49217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49214200-49217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49214200-49218000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:49214200-49220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:49214200-49224000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:49214400-49216200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:49214400-49216800	Enhancers	Left Ventricle	heart
37	chr3:49214400-49217200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:49214400-49217800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:49214600-49216200	Weak transcription	Placenta	Placenta
40	chr3:49214800-49216000	Enhancers	Right Atrium	heart
41	chr3:49214800-49217800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:49214800-49221400	Weak transcription	Fetal Lung	lung
43	chr3:49214800-49228600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:49215000-49217000	Enhancers	Right Ventricle	heart
45	chr3:49215000-49217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:49215000-49217600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:49215000-49225400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:49215200-49216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:49215200-49216800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:49215200-49217400	Weak transcription	Fetal Intestine Large	intestine

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