Variant report

Variant	rs4974081
Chromosome Location	chr3:49070499-49070500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:49069727-49070559	SK-N-SH	brain:	n/a	chr3:49070256-49070267

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49067951..49070552-chr3:49199245..49201626,2	K562	blood:

Variant related genes	Relation type
IMPDH2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11130181	0.91[EUR][1000 genomes]
rs11130183	0.82[CEU][hapmap]
rs11707968	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12715430	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13084037	1.00[YRI][hapmap]
rs13099075	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3087866	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4292260	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4955411	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4955416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4955426	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4955439	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs62259536	0.82[EUR][1000 genomes]
rs6414614	0.96[EUR][1000 genomes]
rs6446200	0.87[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446247	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6446256	0.85[CEU][hapmap]
rs6446257	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs6769821	0.82[CEU][hapmap]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787808	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6798112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7100	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7372883	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7429661	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs7434187	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7621347	0.89[EUR][1000 genomes]
rs7653408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs9810318	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9834003	0.82[CEU][hapmap]
rs9864243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9865051	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][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	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

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs4974081	AMT	cis	cerebellum	SCAN
rs4974081	DALRD3	cis	cerebellum	SCAN
rs4974081	TLR9	cis	parietal	SCAN
rs4974081	WDR6	cis	Nerve Tibial	GTEx
rs4974081	LZTFL1	cis	cerebellum	SCAN
rs4974081	P4HTM	cis	lung	GTEx
rs4974081	NCKIPSD	cis	parietal	SCAN
rs4974081	AMT	cis	Adipose Subcutaneous	GTEx
rs4974081	WDR6	cis	Muscle Skeletal	GTEx
rs4974081	PHF7	cis	parietal	SCAN
rs4974081	NICN1-AS1	cis	Thyroid	GTEx
rs4974081	P4HTM	cis	parietal	SCAN
rs4974081	AMT	cis	multi-tissue	Pritchard
rs4974081	ZNF589	cis	parietal	SCAN
rs4974081	NCKIPSD	cis	Nerve Tibial	GTEx
rs4974081	DALRD3	cis	parietal	SCAN
rs4974081	WDR6	cis	multi-tissue	Pritchard
rs4974081	AMT	cis	Whole Blood	GTEx
rs4974081	AMT	cis	Thyroid	GTEx
rs4974081	AMT	cis	parietal	SCAN
rs4974081	QRICH1	cis	cerebellum	SCAN
rs4974081	AMT	cis	Artery Tibial	GTEx
rs4974081	AMT	cis	lung	GTEx
rs4974081	GPX1	cis	parietal	SCAN
rs4974081	NICN1	cis	cerebellum	SCAN
rs4974081	NICN1	cis	multi-tissue	Pritchard
rs4974081	ARIH2	cis	Thyroid	GTEx
rs4974081	AMT	cis	lymphoblastoid	seeQTL
rs4974081	AMT	cis	Artery Aorta	GTEx
rs4974081	NCKIPSD	cis	multi-tissue	Pritchard
rs4974081	IQCF1	cis	cerebellum	SCAN
rs4974081	WDR6	cis	cerebellum	SCAN
rs4974081	AMT	cis	Nerve Tibial	GTEx
rs4974081	NICN1	cis	Thyroid	GTEx
rs4974081	WDR6	cis	parietal	SCAN
rs4974081	NICN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49067000-49071200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49067000-49074200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:49067200-49072000	Weak transcription	Small Intestine	intestine
6	chr3:49067200-49072200	Weak transcription	Fetal Brain Male	brain
7	chr3:49067200-49074800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:49067200-49078600	Weak transcription	Psoas Muscle	Psoas
9	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
11	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:49067400-49071000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:49067400-49071800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:49067400-49072400	Strong transcription	Spleen	Spleen
15	chr3:49067400-49072600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49067400-49073200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr3:49067400-49073600	Strong transcription	HUVEC	blood vessel
18	chr3:49067400-49074000	Strong transcription	NHDF-Ad	bronchial
19	chr3:49067400-49074800	Strong transcription	Hela-S3	cervix
20	chr3:49067400-49075000	Strong transcription	HepG2	liver
21	chr3:49067400-49075400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:49067400-49075400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:49067400-49075600	Strong transcription	NHEK	skin
24	chr3:49067400-49076400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:49067400-49077200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:49067400-49079800	Strong transcription	Placenta	Placenta
27	chr3:49067400-49085000	Strong transcription	Brain Germinal Matrix	brain
28	chr3:49067400-49085600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:49067400-49085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:49067400-49085600	Strong transcription	Fetal Intestine Large	intestine
31	chr3:49067400-49086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:49067400-49086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
37	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
38	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
39	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:49067600-49071600	Strong transcription	Brain Angular Gyrus	brain
42	chr3:49067600-49072400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:49067600-49072400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:49067600-49072600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr3:49067600-49073600	Strong transcription	Fetal Brain Female	brain
46	chr3:49067600-49074200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:49067600-49074200	Strong transcription	GM12878-XiMat	blood
48	chr3:49067600-49074400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:49067600-49074400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:49067600-49074600	Strong transcription	Rectal Mucosa Donor 29	rectum

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