Variant report

Variant	rs9830730
Chromosome Location	chr3:49675875-49675876
allele	C/G
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	CHD2	chr3:49675874-49676230	Hela-S3	cervix:	n/a	n/a
2	FOSL2	chr3:49675873-49676265	A549	lung:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
3	JUN	chr3:49675765-49676476	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073 chr3:49676448-49676460
4	JUND	chr3:49675847-49676286	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
5	FOSL1	chr3:49675781-49676305	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676062-49676073 chr3:49676064-49676073
6	POLR2A	chr3:49675819-49676135	K562	blood:	n/a	n/a
7	ATF3	chr3:49675821-49676257	K562	blood:	n/a	chr3:49676058-49676072
8	JUN	chr3:49675872-49676237	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
9	MAZ	chr3:49675867-49676258	Hela-S3	cervix:	n/a	chr3:49676189-49676200 chr3:49676063-49676072
10	FOSL1	chr3:49675808-49676563	HCT-116	colon:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676062-49676073 chr3:49676064-49676073 chr3:49676448-49676460
11	GTF2F1	chr3:49675863-49676248	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:49675813-49676272	HCT-116	colon:	n/a	n/a
13	SMARCC1	chr3:49675867-49676484	Hela-S3	cervix:	n/a	chr3:49676063-49676072
14	RCOR1	chr3:49675873-49676305	Hela-S3	cervix:	n/a	n/a
15	EP300	chr3:49675874-49676192	K562	blood:	n/a	chr3:49676063-49676072
16	CBX3	chr3:49675774-49676157	K562	blood:	n/a	n/a
17	E2F6	chr3:49675819-49676033	K562	blood:	n/a	n/a
18	ZBTB7A	chr3:49675852-49676204	K562	blood:	n/a	n/a
19	JUND	chr3:49675858-49676321	Hela-S3	cervix:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
20	SIN3AK20	chr3:49675866-49676137	K562	blood:	n/a	n/a
21	TCF12	chr3:49675764-49676281	ECC-1	luminal epithelium:	n/a	n/a
22	MEF2A	chr3:49675754-49676359	K562	blood:	n/a	chr3:49676064-49676072 chr3:49676034-49676049
23	JUND	chr3:49675743-49676503	HCT-116	colon:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073 chr3:49676448-49676460
24	HCFC1	chr3:49675767-49676429	Hela-S3	cervix:	n/a	n/a
25	JUND	chr3:49675755-49676350	SK-N-SH	brain:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
26	MAX	chr3:49675814-49676383	K562	blood:	n/a	chr3:49676189-49676200 chr3:49676063-49676072
27	MYC	chr3:49675849-49676203	K562	blood:	n/a	chr3:49676189-49676200 chr3:49676063-49676072
28	RCOR1	chr3:49675850-49676232	K562	blood:	n/a	n/a
29	TEAD4	chr3:49675874-49676152	K562	blood:	n/a	n/a
30	MAZ	chr3:49675817-49676254	K562	blood:	n/a	chr3:49676189-49676200 chr3:49676063-49676072
31	SMC3	chr3:49675849-49676323	Hela-S3	cervix:	n/a	n/a
32	TEAD4	chr3:49675822-49676270	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49673401..49676066-chr3:49680626..49682586,2	MCF-7	breast:
2	chr3:49666488..49668184-chr3:49675281..49676977,2	K562	blood:

Variant related genes	Relation type
BSN	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	0.94[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	0.88[CEU][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs13096480	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs1491985	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1532204	0.94[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.94[CEU][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2329021	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap]
rs4241405	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap]
rs4855885	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754265	0.81[EUR][1000 genomes]
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]
rs62261249	1.00[ASN][1000 genomes]
rs62262671	0.81[EUR][1000 genomes]
rs62262672	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.80[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap]
rs7628207	1.00[CEU][hapmap]
rs7637711	1.00[CEU][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap]
rs9835157	1.00[CEU][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap]
rs9860055	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap]
rs9870858	1.00[CEU][hapmap]
rs9871024	1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv3812	chr3:49669773-49680587	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9830730	AMT	cis	lung	GTEx
rs9830730	RNF123	cis	Artery Tibial	GTEx
rs9830730	AMT	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49655600-49676200	Weak transcription	HepG2	liver
2	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49660800-49682600	Weak transcription	Liver	Liver
4	chr3:49661600-49692400	Weak transcription	Ovary	ovary
5	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
6	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
7	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
9	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
14	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:49672800-49676000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49673400-49676000	Enhancers	K562	blood
18	chr3:49673400-49676200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:49673800-49676400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:49673800-49676800	Enhancers	NHEK	skin
23	chr3:49673800-49692400	Weak transcription	Gastric	stomach
24	chr3:49674000-49676000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:49674000-49676000	Enhancers	Spleen	Spleen
26	chr3:49674000-49676200	Enhancers	Hela-S3	cervix
27	chr3:49674000-49676600	Enhancers	HMEC	breast
28	chr3:49674200-49676400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:49674400-49676400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:49674400-49676400	Enhancers	Fetal Muscle Trunk	muscle
31	chr3:49674400-49676400	Enhancers	HSMMtube	muscle
32	chr3:49674400-49680000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:49674600-49677600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:49675000-49676400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:49675000-49676400	Enhancers	Placenta	Placenta
36	chr3:49675000-49679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:49675000-49680400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:49675400-49676400	Enhancers	Fetal Muscle Leg	muscle
39	chr3:49675400-49676600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:49675400-49677000	Weak transcription	Brain Anterior Caudate	brain
41	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:49675600-49677000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:49675600-49679600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:49675800-49676200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49675800-49676200	Enhancers	Esophagus	oesophagus
46	chr3:49675800-49676400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:49675800-49676400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:49675800-49676400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49675800-49676600	Enhancers	HSMM	muscle
50	chr3:49675800-49676600	Enhancers	NH-A	brain

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