Variant report

Variant	rs60528401
Chromosome Location	chr3:194876128-194876129
allele	A/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	NFIC	chr3:194875657-194876293	SK-N-SH	brain:	n/a	chr3:194876041-194876069
2	EP300	chr3:194875587-194876161	HepG2	liver:	n/a	chr3:194875890-194875899
3	NR3C1	chr3:194875819-194876275	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr3:194875855-194876142	HepG2	liver:	n/a	n/a
5	MAX	chr3:194875576-194876360	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr3:194875706-194876146	K562	blood:	n/a	n/a
7	GATA3	chr3:194875622-194876426	SK-N-SH	brain:	n/a	chr3:194876256-194876266
8	MAZ	chr3:194875714-194876159	HepG2	liver:	n/a	n/a
9	FOXM1	chr3:194875269-194876169	GM12878	blood:	n/a	n/a
10	TEAD4	chr3:194875582-194876240	SK-N-SH	brain:	n/a	n/a
11	TCF7L2	chr3:194875399-194876243	PANC-1	pancreas:	n/a	n/a
12	HEY1	chr3:194875798-194876284	HepG2	liver:	n/a	n/a
13	MAZ	chr3:194875842-194876147	GM12878	blood:	n/a	n/a
14	PBX3	chr3:194875751-194876299	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:194875703-194876325	SK-N-SH	brain:	n/a	n/a
16	MYC	chr3:194875776-194876192	MCF10A-Er-Src	breast:	n/a	n/a
17	TAF1	chr3:194875880-194876219	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:194875873-194876141	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:194874776-194877542	HUVEC	blood vessel:	n/a	n/a
20	SP1	chr3:194875560-194876259	HepG2	liver:	n/a	chr3:194875700-194875714
21	CEBPB	chr3:194875865-194876139	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:194874910-194876935	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:194875515-194876288	HUVEC	blood vessel:	n/a	n/a
24	REST	chr3:194875956-194876227	SK-N-SH	brain:	n/a	chr3:194876053-194876073
25	POLR2A	chr3:194875162-194876191	GM12891	blood:	n/a	n/a
26	STAT3	chr3:194875861-194876143	MCF10A-Er-Src	breast:	n/a	chr3:194875885-194875893
27	ELF1	chr3:194875607-194876182	GM12878	blood:	n/a	chr3:194875890-194875901
28	TEAD4	chr3:194875662-194876273	ECC-1	luminal epithelium:	n/a	n/a
29	MBD4	chr3:194875672-194876226	HepG2	liver:	n/a	n/a
30	RAD21	chr3:194875703-194876194	HepG2	liver:	n/a	n/a
31	MYC	chr3:194875677-194876240	HepG2	liver:	n/a	n/a
32	STAT5A	chr3:194875017-194876194	GM12878	blood:	n/a	chr3:194875694-194875706 chr3:194875885-194875893
33	REST	chr3:194875815-194876185	SK-N-SH	brain:	n/a	chr3:194876053-194876073
34	PML	chr3:194875553-194876210	GM12878	blood:	n/a	n/a
35	TCF12	chr3:194875545-194876536	ECC-1	luminal epithelium:	n/a	chr3:194876448-194876455
36	POLR2A	chr3:194875952-194876671	K562	blood:	n/a	n/a
37	POLR2A	chr3:194875830-194876146	GM12878	blood:	n/a	n/a
38	FOXA1	chr3:194875620-194876141	HepG2	liver:	n/a	n/a
39	JUN	chr3:194875661-194876201	HUVEC	blood vessel:	n/a	n/a
40	TEAD4	chr3:194875659-194876271	ECC-1	luminal epithelium:	n/a	n/a
41	MYBL2	chr3:194875581-194876209	HepG2	liver:	n/a	n/a
42	BHLHE40	chr3:194875626-194876133	HepG2	liver:	n/a	n/a
43	ELF1	chr3:194875549-194876224	GM12878	blood:	n/a	chr3:194875890-194875901
44	PBX3	chr3:194875688-194876358	SK-N-SH	brain:	n/a	n/a
45	TEAD4	chr3:194875552-194876243	HepG2	liver:	n/a	n/a
46	NFIC	chr3:194875538-194876177	HepG2	liver:	n/a	chr3:194876041-194876069
47	RXRA	chr3:194875583-194876311	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr3:194872900-194876209	GM12891	blood:	n/a	n/a
49	MYC	chr3:194875589-194876172	HUVEC	blood vessel:	n/a	n/a
50	FOS	chr3:194875817-194876162	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194865591..194868396-chr3:194874419..194877392,2	K562	blood:
2	chr3:194840474..194843424-chr3:194874062..194876666,2	K562	blood:
3	chr3:194862609..194865401-chr3:194875415..194878786,3	K562	blood:
4	chr3:194837632..194840596-chr3:194875671..194877236,2	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000244314	Chromatin interaction
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10433328	0.93[ASN][1000 genomes]
rs10433329	0.98[ASN][1000 genomes]
rs10433330	0.98[ASN][1000 genomes]
rs10933700	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933701	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12491661	0.95[ASN][1000 genomes]
rs12491663	0.89[ASN][1000 genomes]
rs2004553	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088040	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088041	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2410844	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2410846	0.86[ASN][1000 genomes]
rs28613110	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677662	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677811	0.98[ASN][1000 genomes]
rs4677814	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59556963	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59834989	0.80[AMR][1000 genomes]
rs6437460	0.95[ASN][1000 genomes]
rs6799346	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73206648	0.93[ASN][1000 genomes]
rs73206650	0.93[ASN][1000 genomes]
rs73206651	0.98[ASN][1000 genomes]
rs7628775	0.88[ASN][1000 genomes]
rs7637593	0.88[ASN][1000 genomes]
rs7653355	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903309	0.93[ASN][1000 genomes]
rs903311	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809570	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9825521	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
2	chr3:194862400-194897800	Weak transcription	Dnd41	blood
3	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
4	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
5	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
6	chr3:194869600-194876400	Enhancers	NHDF-Ad	bronchial
7	chr3:194869800-194876600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:194870800-194877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:194871000-194877200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:194871000-194880800	Enhancers	HUVEC	blood vessel
11	chr3:194871400-194877800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:194871600-194877600	Enhancers	Fetal Intestine Large	intestine
14	chr3:194871600-194881200	Weak transcription	Liver	Liver
15	chr3:194871800-194876200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:194871800-194876400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:194871800-194876600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:194871800-194876800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:194871800-194876800	Enhancers	Osteobl	bone
20	chr3:194871800-194877000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:194871800-194878200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:194872000-194877000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:194872000-194877200	Enhancers	Stomach Mucosa	stomach
25	chr3:194872000-194877400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:194872400-194877600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:194872600-194876200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr3:194872800-194876400	Enhancers	Placenta	Placenta
32	chr3:194872800-194877400	Enhancers	Right Atrium	heart
33	chr3:194872800-194877600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:194873000-194876200	Enhancers	NH-A	brain
35	chr3:194873000-194876800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:194873000-194876800	Enhancers	Esophagus	oesophagus
37	chr3:194873000-194877200	Enhancers	Ovary	ovary
38	chr3:194873000-194877600	Enhancers	Adipose Nuclei	Adipose
39	chr3:194873000-194877800	Enhancers	Left Ventricle	heart
40	chr3:194873000-194884400	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:194873000-194884600	Enhancers	Fetal Thymus	thymus
42	chr3:194873200-194876400	Enhancers	Brain Anterior Caudate	brain
43	chr3:194873600-194876200	Enhancers	Fetal Brain Female	brain
44	chr3:194873600-194876800	Enhancers	Brain Cingulate Gyrus	brain
45	chr3:194873600-194877400	Enhancers	Right Ventricle	heart
46	chr3:194873600-194877600	Enhancers	Colonic Mucosa	Colon
47	chr3:194873600-194877600	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:194873800-194876400	Enhancers	Brain Substantia Nigra	brain
49	chr3:194873800-194876800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:194873800-194877000	Enhancers	Brain Inferior Temporal Lobe	brain

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