Variant report

Variant	rs6788650
Chromosome Location	chr3:48749543-48749544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48731283..48735780-chr3:48749291..48752542,4	MCF-7	breast:
2	chr3:48699198..48701664-chr3:48748903..48750762,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228350	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:78)

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	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	1.00[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]
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]
rs12107252	0.80[LWK][hapmap];0.82[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];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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[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]
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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];0.86[EUR][1000 genomes]
rs6446252	0.92[CEU][hapmap]
rs6446253	0.92[CEU][hapmap]
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	0.83[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];0.85[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	0.86[AMR][1000 genomes];0.92[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];0.83[YRI][hapmap]
rs9812200	0.90[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	1.00[YRI][hapmap]
rs9841602	1.00[YRI][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];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]

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:33)

SNP	Gene	Cis/trans	Tissue	Source
rs6788650	WDR6	cis	parietal	SCAN
rs6788650	CCDC36	cis	Artery Tibial	GTEx
rs6788650	NCKIPSD	cis	cerebellum	SCAN
rs6788650	DALRD3	cis	cerebellum	SCAN
rs6788650	CCDC71	cis	cerebellum	SCAN
rs6788650	WDR6	cis	Whole Blood	GTEx
rs6788650	NCKIPSD	cis	Nerve Tibial	GTEx
rs6788650	TLR9	cis	parietal	SCAN
rs6788650	ZNF589	cis	cerebellum	SCAN
rs6788650	NCKIPSD	cis	Whole Blood	GTEx
rs6788650	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6788650	P4HTM	cis	parietal	SCAN
rs6788650	WDR6	cis	lung	GTEx
rs6788650	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6788650	NICN1	cis	Thyroid	GTEx
rs6788650	DALRD3	cis	parietal	SCAN
rs6788650	C3orf62	cis	cerebellum	SCAN
rs6788650	NICN1-AS1	cis	Thyroid	GTEx
rs6788650	NCKIPSD	cis	parietal	SCAN
rs6788650	WDR6	cis	Esophagus Mucosa	GTEx
rs6788650	WDR6	cis	Adipose Subcutaneous	GTEx
rs6788650	AMT	cis	cerebellum	SCAN
rs6788650	WDR6	cis	lymphoblastoid	seeQTL
rs6788650	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6788650	WDR6	cis	Muscle Skeletal	GTEx
rs6788650	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6788650	WDR6	cis	Nerve Tibial	GTEx
rs6788650	AMT	cis	Thyroid	GTEx
rs6788650	ZNF589	cis	parietal	SCAN
rs6788650	WDR6	cis	cerebellum	SCAN
rs6788650	AMT	cis	parietal	SCAN
rs6788650	NCKIPSD	cis	Muscle Skeletal	GTEx
rs6788650	WDR6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
2	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:48741400-48750600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:48741600-48749600	Strong transcription	Primary B cells from cord blood	blood
7	chr3:48741600-48750600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr3:48741600-48752400	Strong transcription	Fetal Intestine Large	intestine
9	chr3:48741800-48751800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:48741800-48752400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:48741800-48752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:48742800-48750000	Strong transcription	Placenta	Placenta
13	chr3:48742800-48750800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:48743000-48749600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:48743000-48752400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:48743600-48750600	Strong transcription	Hela-S3	cervix
18	chr3:48743600-48751200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:48743600-48751800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:48743600-48752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr3:48744600-48749600	Strong transcription	HUVEC	blood vessel
23	chr3:48744600-48751000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:48744600-48751200	Genic enhancers	Primary T cells from cord blood	blood
25	chr3:48744800-48750600	Genic enhancers	Brain Germinal Matrix	brain
26	chr3:48745600-48751200	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr3:48745600-48752800	Weak transcription	Small Intestine	intestine
28	chr3:48745800-48753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:48746400-48749800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:48746600-48752400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:48746600-48752400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:48746600-48752600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:48746800-48750000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:48746800-48750600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:48746800-48750600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:48746800-48750600	Strong transcription	Fetal Intestine Small	intestine
37	chr3:48746800-48750600	Strong transcription	Fetal Lung	lung
38	chr3:48746800-48752200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr3:48746800-48752200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:48747000-48750000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:48747000-48750600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:48747000-48751800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:48747000-48751800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:48747000-48752200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:48747000-48752200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:48747000-48752600	Weak transcription	A549	lung
47	chr3:48747200-48750200	Strong transcription	NHDF-Ad	bronchial
48	chr3:48747200-48751800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:48747400-48749600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:48747400-48749600	Strong transcription	NH-A	brain

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