Variant report

Variant	rs7617480
Chromosome Location	chr3:49210732-49210733
allele	A/C
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	NFIC	chr3:49210685-49211332	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
2	MEF2A	chr3:49210715-49211082	K562	blood:	n/a	chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
3	REST	chr3:49210427-49211993	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:49210676-49211201	H1-neurons	neurons:	n/a	n/a
5	MEF2A	chr3:49210626-49211078	K562	blood:	n/a	chr3:49210627-49210635 chr3:49210883-49210898 chr3:49210883-49210899 chr3:49210883-49210898 chr3:49210885-49210896 chr3:49210879-49210900 chr3:49210886-49210895 chr3:49210882-49210898
6	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
7	POLR2A	chr3:49210721-49211608	H1-neurons	neurons:	n/a	n/a
8	NFIC	chr3:49210601-49211651	SK-N-SH	brain:	n/a	chr3:49210992-49211008 chr3:49210921-49210938
9	TBL1XR1	chr3:49210624-49211122	K562	blood:	n/a	n/a
10	ZC3H11A	chr3:49210724-49210758	K562	blood:	n/a	n/a
11	POLR2A	chr3:49210665-49210807	K562	blood:	n/a	n/a
12	NR2F2	chr3:49210558-49211119	K562	blood:	n/a	n/a
13	EP300	chr3:49210709-49211171	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

Variant related genes	Relation type
KLHDC8B	TF binding region
ENSG00000185909	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000270441	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10154992	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130181	0.91[AFR][1000 genomes]
rs11130183	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.87[ASW][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs12637346	0.81[AMR][1000 genomes]
rs13084037	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3212	0.86[YRI][hapmap]
rs3448	1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs35713889	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4292260	0.93[ASW][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4521268	0.82[YRI][hapmap]
rs4955411	0.93[ASW][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955416	0.93[ASW][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4955417	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs4955421	0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955439	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955443	0.80[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs4974080	0.86[YRI][hapmap]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446205	0.89[YRI][hapmap]
rs6446256	0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6778080	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6779394	0.93[YRI][hapmap]
rs6781790	0.82[YRI][hapmap]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs73088137	1.00[ASN][1000 genomes]
rs7373790	0.83[AFR][1000 genomes]
rs7429661	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432989	0.93[YRI][hapmap]
rs7619016	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7621015	0.82[YRI][hapmap]
rs7626076	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7626445	0.82[YRI][hapmap]
rs7631586	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974495	1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834003	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840050	0.86[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9846123	0.82[YRI][hapmap]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.82[TSI][hapmap]
rs9867285	1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	21102462	GWAS catalog

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs7617480	AMT	cis	lymphoblastoid	seeQTL
rs7617480	AMT	cis	multi-tissue	Pritchard
rs7617480	ZNF589	cis	parietal	SCAN
rs7617480	WDR6	cis	Heart Left Ventricle	GTEx
rs7617480	AMT	cis	Nerve Tibial	GTEx
rs7617480	NICN1	cis	cerebellum	SCAN
rs7617480	NME6	cis	cerebellum	SCAN
rs7617480	SEMA3G	cis	cerebellum	SCAN
rs7617480	AMT	cis	Thyroid	GTEx
rs7617480	NICN1	cis	multi-tissue	Pritchard
rs7617480	WDR6	cis	cerebellum	SCAN
rs7617480	QRICH1	cis	cerebellum	SCAN
rs7617480	AMT	cis	cerebellum	SCAN
rs7617480	AMT	cis	Whole Blood	GTEx
rs7617480	DALRD3	cis	cerebellum	SCAN
rs7617480	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7617480	WDR6	cis	multi-tissue	Pritchard
rs7617480	NICN1-AS1	cis	Thyroid	GTEx
rs7617480	P4HTM	cis	parietal	SCAN
rs7617480	AMT	cis	parietal	SCAN
rs7617480	WDR6	cis	Muscle Skeletal	GTEx
rs7617480	GNL3	cis	parietal	SCAN
rs7617480	WDR6	cis	lung	GTEx
rs7617480	WDR6	cis	parietal	SCAN
rs7617480	WDR6	cis	Nerve Tibial	GTEx
rs7617480	GPX1	cis	parietal	SCAN
rs7617480	DALRD3	cis	parietal	SCAN
rs7617480	GMPPB	cis	parietal	SCAN
rs7617480	NICN1	cis	Thyroid	GTEx
rs7617480	GNL3	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49208200-49211200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:49208200-49211400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:49208200-49212000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:49209200-49211800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49209200-49212000	Flanking Active TSS	Fetal Brain Female	brain
6	chr3:49209200-49212400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:49209400-49211200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:49209400-49211200	Flanking Active TSS	K562	blood
9	chr3:49209400-49211400	Flanking Active TSS	HepG2	liver
10	chr3:49209400-49211600	Flanking Active TSS	Fetal Lung	lung
11	chr3:49209400-49211600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:49209600-49210800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:49209600-49210800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:49209600-49210800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:49209600-49210800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr3:49209600-49211000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr3:49209600-49211000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:49209600-49211200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:49209600-49211400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49209600-49211400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:49209600-49211400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr3:49209600-49211600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:49209600-49211600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:49209600-49211800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
25	chr3:49209600-49211800	Flanking Active TSS	HSMMtube	muscle
26	chr3:49209600-49212000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:49209600-49212000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
28	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:49209800-49210800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:49209800-49210800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
31	chr3:49209800-49210800	Weak transcription	A549	lung
32	chr3:49209800-49211200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:49209800-49211200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:49209800-49211200	Flanking Active TSS	HSMM	muscle
35	chr3:49209800-49211400	Flanking Active TSS	Left Ventricle	heart
36	chr3:49209800-49211400	Flanking Active TSS	Right Ventricle	heart
37	chr3:49209800-49212000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr3:49209800-49212400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:49209800-49212600	Enhancers	Fetal Brain Male	brain
40	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:49210000-49210800	Flanking Active TSS	Fetal Heart	heart
42	chr3:49210000-49210800	Enhancers	Pancreas	Pancrea
43	chr3:49210000-49211000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:49210000-49211200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:49210000-49211200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:49210000-49211400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:49210000-49211400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
48	chr3:49210000-49211400	Enhancers	Brain Substantia Nigra	brain
49	chr3:49210000-49211600	Weak transcription	Primary T cells from cord blood	blood
50	chr3:49210000-49211600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links