Variant report

Variant	rs13434258
Chromosome Location	chr3:48738491-48738492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48736950..48739890-chr3:48741169..48743085,3	K562	blood:
2	chr3:48723186..48725307-chr3:48738132..48740466,2	MCF-7	breast:
3	chr3:48736967..48739761-chr3:49056204..49057808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213672	Chromatin interaction
ENSG00000199032	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap]
rs1048940	0.84[CEU][hapmap]
rs10780033	1.00[CHD][hapmap]
rs10865952	0.95[ASN][1000 genomes]
rs11130176	1.00[CHD][hapmap]
rs11557629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs11715177	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[ASN][1000 genomes]
rs11719291	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs11920534	1.00[CHD][hapmap]
rs11928552	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12107252	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs12107418	1.00[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13060933	0.83[GIH][hapmap]
rs13063223	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063312	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs13070798	1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318132	0.90[ASW][hapmap]
rs13319651	0.83[GIH][hapmap]
rs13324119	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324142	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs13324950	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080289	1.00[GIH][hapmap]
rs17080319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006871	0.83[GIH][hapmap]
rs2276850	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs2276852	1.00[GIH][hapmap]
rs2286651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286652	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2310996	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs28452701	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2854394	0.83[GIH][hapmap]
rs28567949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs34096717	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34153629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3821876	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs3969942	0.83[GIH][hapmap]
rs4077495	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974079	1.00[CHD][hapmap]
rs4974085	1.00[CHD][hapmap]
rs4974087	1.00[CHD][hapmap]
rs56735597	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61137521	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6768448	0.85[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6781283	0.83[GIH][hapmap]
rs6788650	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6791542	1.00[CHD][hapmap]
rs6792156	1.00[GIH][hapmap]
rs6792525	0.83[GIH][hapmap]
rs68042649	0.85[EUR][1000 genomes]
rs6806059	0.83[GIH][hapmap]
rs73078362	0.81[EUR][1000 genomes]
rs740787	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs7428949	1.00[JPT][hapmap]
rs7430501	1.00[CHD][hapmap]
rs7431710	1.00[CHD][hapmap]
rs7431857	1.00[CHD][hapmap]
rs7623023	1.00[CHD][hapmap]
rs7627404	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7631574	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs7647813	1.00[CHD][hapmap]
rs7649458	1.00[CHD][hapmap]
rs9311430	1.00[CHD][hapmap]
rs9311433	1.00[CHD][hapmap]
rs9311434	1.00[CHD][hapmap]
rs9682444	0.87[CHD][hapmap]
rs9755490	0.87[CHD][hapmap]
rs9809222	0.85[EUR][1000 genomes]
rs9810549	0.83[GIH][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9812200	1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821797	0.85[EUR][1000 genomes]
rs9830581	1.00[GIH][hapmap]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9836462	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9837687	0.83[GIH][hapmap]
rs9841602	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9843316	1.00[GIH][hapmap]
rs9848203	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850102	0.83[GIH][hapmap]
rs9854034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868809	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs9869698	0.83[GIH][hapmap]
rs9871180	1.00[GIH][hapmap]
rs9873726	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9876848	1.00[CHD][hapmap]
rs9877542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882962	0.83[GIH][hapmap]

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	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	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs13434258	WDR6	cis	lung	GTEx
rs13434258	C3orf62	cis	parietal	SCAN
rs13434258	WDR6	cis	parietal	SCAN
rs13434258	LRRC2	cis	cerebellum	SCAN
rs13434258	WDR6	cis	lymphoblastoid	seeQTL
rs13434258	CSPG5	cis	parietal	SCAN
rs13434258	ALAS1	cis	cerebellum	SCAN
rs13434258	C3orf62	cis	cerebellum	SCAN
rs13434258	NCKIPSD	cis	parietal	SCAN
rs13434258	WDR6	cis	Adipose Subcutaneous	GTEx
rs13434258	WDR6	cis	Esophagus Mucosa	GTEx
rs13434258	WDR6	cis	Whole Blood	GTEx
rs13434258	RNF123	cis	parietal	SCAN
rs13434258	WDR6	cis	cerebellum	SCAN
rs13434258	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
2	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
3	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:48725000-48740800	Strong transcription	Dnd41	blood
8	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
11	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
12	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
16	chr3:48733200-48738600	Strong transcription	Fetal Lung	lung
17	chr3:48733200-48738800	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:48733200-48740800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
20	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
22	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
23	chr3:48733600-48739200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:48734000-48738600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
26	chr3:48734200-48740200	Weak transcription	Fetal Heart	heart
27	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:48734400-48739800	Weak transcription	A549	lung
29	chr3:48734400-48740200	Weak transcription	NHDF-Ad	bronchial
30	chr3:48734400-48740800	Strong transcription	Fetal Intestine Large	intestine
31	chr3:48734400-48741600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:48734400-48741600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:48734400-48744600	Weak transcription	NHLF	lung
34	chr3:48734400-48745600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:48734400-48746000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:48734400-48746000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:48734400-48746200	Weak transcription	Gastric	stomach
38	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
39	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:48734800-48740800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:48735200-48738800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr3:48735200-48738800	Strong transcription	Placenta	Placenta
43	chr3:48735200-48740600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr3:48735400-48738600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:48735400-48738800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:48735400-48740200	Strong transcription	Fetal Stomach	stomach
47	chr3:48735600-48739800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:48735600-48740200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:48735800-48738600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:48735800-48738800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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