Variant report

Variant	rs2404487
Chromosome Location	chr7:99038057-99038058
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	USF1	chr7:99037815-99038060	H1-hESC	embryonic stem cell:	n/a	chr7:99037930-99037941
2	CEBPB	chr7:99037822-99038190	A549	lung:	n/a	chr7:99038027-99038038
3	POLR2A	chr7:99037900-99038264	HepG2	liver:	n/a	n/a
4	CEBPB	chr7:99037850-99038231	HepG2	liver:	n/a	chr7:99038027-99038038
5	POLR2A	chr7:99037728-99038135	K562	blood:	n/a	n/a
6	CEBPB	chr7:99037853-99038245	IMR90	lung:	n/a	chr7:99038027-99038038
7	POLR2A	chr7:99038011-99038075	HUVEC	blood vessel:	n/a	n/a
8	CEBPB	chr7:99037886-99038136	HepG2	liver:	n/a	chr7:99038027-99038038
9	CEBPB	chr7:99037849-99038208	A549	lung:	n/a	chr7:99038027-99038038
10	CEBPB	chr7:99037841-99038231	A549	lung:	n/a	chr7:99038027-99038038
11	CEBPB	chr7:99037792-99038280	MCF-7	breast:	n/a	chr7:99038027-99038038
12	CEBPB	chr7:99037902-99038195	Hela-S3	cervix:	n/a	chr7:99038027-99038038
13	CEBPB	chr7:99037830-99038186	K562	blood:	n/a	chr7:99038027-99038038
14	FOXA2	chr7:99037846-99038069	HepG2	liver:	n/a	n/a
15	POLR2A	chr7:99035899-99038179	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr7:99035445-99038169	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr7:99038004-99038156	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr7:99037731-99038147	K562	blood:	n/a	n/a
19	CEBPB	chr7:99037847-99038223	HepG2	liver:	n/a	chr7:99038027-99038038
20	CEBPB	chr7:99037844-99038218	K562	blood:	n/a	chr7:99038027-99038038
21	CEBPB	chr7:99037877-99038213	H1-hESC	embryonic stem cell:	n/a	chr7:99038027-99038038

No.	Distal block	Cell Line	Cell type
1	chr7:99036051..99038082-chr7:99079952..99081854,3	K562	blood:
2	chr7:99008645..99011330-chr7:99036359..99039743,4	K562	blood:
3	chr7:98940912..98943570-chr7:99037512..99039699,2	K562	blood:
4	chr7:98739484..98741856-chr7:99035435..99038061,2	K562	blood:
5	chr7:99004207..99009187-chr7:99032699..99039268,13	MCF-7	breast:
6	chr7:99035431..99038374-chr7:99696976..99699327,2	K562	blood:
7	chr7:99034720..99038160-chr7:99048984..99054018,5	MCF-7	breast:
8	chr7:99035887..99038153-chr7:99062281..99064908,3	MCF-7	breast:
9	chr7:99036970..99039265-chr7:99039739..99041583,2	MCF-7	breast:
10	chr7:99030944..99035080-chr7:99035226..99039444,6	MCF-7	breast:

Variant related genes	Relation type
PTCD1	TF binding region
ENSG00000214314	TF binding region
CPSF4	TF binding region
ENSG00000166508	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000228335	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000198742	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000214314	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10251282	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279308	0.95[ASN][1000 genomes]
rs1045012	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734	0.89[ASN][1000 genomes]
rs11972210	0.83[ASN][1000 genomes]
rs11978089	0.95[ASN][1000 genomes]
rs17161700	0.85[EUR][1000 genomes]
rs17161726	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17854665	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003499	0.95[ASN][1000 genomes]
rs2293256	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404488	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365067	0.89[ASN][1000 genomes]
rs28377312	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460612	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558950	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668326	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28753399	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34943973	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3528	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823813	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41258334	0.89[ASN][1000 genomes]
rs45441991	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45448997	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45451992	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45461000	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45492501	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45529541	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45555335	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45592335	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55927283	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55942267	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167514	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57367781	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57830676	0.83[ASN][1000 genomes]
rs57832867	0.85[EUR][1000 genomes]
rs59240302	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59574285	0.89[ASN][1000 genomes]
rs59672032	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956305	0.89[ASN][1000 genomes]
rs6974831	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6976017	0.89[ASN][1000 genomes]
rs6977165	0.89[ASN][1000 genomes]
rs73397447	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397499	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401507	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401510	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401516	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403247	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73403272	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73403286	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73403290	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73405247	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73711280	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711293	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73711294	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73713507	0.94[ASN][1000 genomes]
rs73713531	0.89[ASN][1000 genomes]
rs73713580	0.89[ASN][1000 genomes]
rs7794068	0.94[ASN][1000 genomes]
rs7805661	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs917152	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952319	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99034800-99038200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:99035200-99038600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:99035400-99038800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:99035600-99038200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:99037000-99038200	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr7:99037000-99038200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
7	chr7:99037000-99038200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr7:99037000-99038200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr7:99037200-99038200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
10	chr7:99037200-99038200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr7:99037200-99038200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:99037200-99038200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:99037200-99038200	Flanking Active TSS	Colon Smooth Muscle	Colon
14	chr7:99037200-99038600	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr7:99037400-99038200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:99037400-99038200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:99037400-99038200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr7:99037400-99038200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:99037400-99038200	Enhancers	Fetal Thymus	thymus
20	chr7:99037400-99038200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr7:99037400-99038200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr7:99037400-99038200	Flanking Active TSS	GM12878-XiMat	blood
23	chr7:99037400-99038200	Transcr. at gene 5' and 3'	Hela-S3	cervix
24	chr7:99037400-99038200	Flanking Active TSS	NH-A	brain
25	chr7:99037400-99038200	Flanking Active TSS	NHEK	skin
26	chr7:99037400-99038600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:99037400-99039200	Enhancers	Spleen	Spleen
28	chr7:99037600-99038200	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:99037600-99038200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr7:99037600-99038200	Enhancers	Primary B cells from peripheral blood	blood
31	chr7:99037600-99038200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:99037600-99038200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:99037600-99038200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:99037600-99038200	Enhancers	Brain Cingulate Gyrus	brain
35	chr7:99037600-99038200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr7:99037600-99038200	Enhancers	Fetal Heart	heart
37	chr7:99037600-99038200	Enhancers	Gastric	stomach
38	chr7:99037600-99038200	Enhancers	Right Atrium	heart
39	chr7:99037600-99038200	Enhancers	Small Intestine	intestine
40	chr7:99037600-99038200	Flanking Active TSS	HepG2	liver
41	chr7:99037600-99038400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr7:99037600-99038600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr7:99037600-99039200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr7:99037600-99039200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:99037800-99038200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
46	chr7:99037800-99038200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
47	chr7:99037800-99038200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:99037800-99038200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr7:99037800-99038200	Enhancers	Primary B cells from cord blood	blood
50	chr7:99037800-99038200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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