Variant report

Variant	rs2405440
Chromosome Location	chr7:99760973-99760974
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	chr7:99760677-99761103	H1-hESC	embryonic stem cell:	n/a	chr7:99760870-99760881
2	MXI1	chr7:99760805-99761104	Hela-S3	cervix:	n/a	n/a
3	MAX	chr7:99760591-99761183	MCF-7	breast:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
4	USF1	chr7:99760630-99761107	K562	blood:	n/a	chr7:99760870-99760881
5	HDAC2	chr7:99760522-99761188	MCF-7	breast:	n/a	chr7:99761102-99761116 chr7:99761101-99761115 chr7:99761098-99761112 chr7:99761103-99761117 chr7:99761099-99761113 chr7:99761096-99761110 chr7:99761100-99761114
6	USF1	chr7:99760531-99761351	HCT-116	colon:	n/a	chr7:99760870-99760881
7	BHLHE40	chr7:99760802-99760980	K562	blood:	n/a	n/a
8	RFX5	chr7:99760732-99761050	Hela-S3	cervix:	n/a	n/a
9	ZNF217	chr7:99760658-99761022	MCF-7	breast:	n/a	n/a
10	USF1	chr7:99760627-99761223	HCT-116	colon:	n/a	chr7:99760870-99760881
11	USF1	chr7:99760694-99761063	A549	lung:	n/a	chr7:99760870-99760881
12	FOS	chr7:99760765-99760995	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr7:99760525-99761144	H1-neurons	neurons:	n/a	n/a
14	USF2	chr7:99760811-99761011	HepG2	liver:	n/a	chr7:99760871-99760882
15	RAD21	chr7:99760796-99761072	Hela-S3	cervix:	n/a	n/a
16	MAX	chr7:99760724-99761061	Hela-S3	cervix:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
17	USF1	chr7:99760768-99761033	GM12878	blood:	n/a	chr7:99760870-99760881
18	MYC	chr7:99760780-99761027	MCF10A-Er-Src	breast:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
19	MAX	chr7:99760616-99761110	K562	blood:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
20	TFAP2C	chr7:99760516-99761149	Hela-S3	cervix:	n/a	chr7:99760856-99760871
21	USF1	chr7:99760732-99760973	A549	lung:	n/a	chr7:99760870-99760881
22	USF1	chr7:99760750-99760979	HepG2	liver:	n/a	chr7:99760870-99760881
23	ZNF384	chr7:99760870-99761256	K562	blood:	n/a	n/a
24	RCOR1	chr7:99760700-99761059	Hela-S3	cervix:	n/a	n/a
25	USF1	chr7:99760605-99761050	A549	lung:	n/a	chr7:99760870-99760881
26	USF1	chr7:99760633-99761092	ECC-1	luminal epithelium:	n/a	chr7:99760870-99760881
27	ZNF384	chr7:99760937-99761223	GM12878	blood:	n/a	n/a
28	MAX	chr7:99760547-99761139	MCF-7	breast:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
29	GTF2F1	chr7:99760760-99761086	Hela-S3	cervix:	n/a	n/a
30	USF2	chr7:99760634-99761093	Hela-S3	cervix:	n/a	chr7:99760871-99760882
31	SMC3	chr7:99760711-99761043	Hela-S3	cervix:	n/a	n/a
32	MAX	chr7:99760708-99761070	Hela-S3	cervix:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881
33	USF1	chr7:99760689-99761071	K562	blood:	n/a	chr7:99760870-99760881
34	POLR2A	chr7:99760698-99761050	HCT-116	colon:	n/a	n/a
35	USF1	chr7:99760616-99761130	ECC-1	luminal epithelium:	n/a	chr7:99760870-99760881
36	TFAP2A	chr7:99760555-99761153	Hela-S3	cervix:	n/a	chr7:99760857-99760869 chr7:99760857-99760869 chr7:99760857-99760869 chr7:99760856-99760871 chr7:99760857-99760869
37	CEBPB	chr7:99760728-99761052	Hela-S3	cervix:	n/a	n/a
38	ZKSCAN1	chr7:99760733-99761016	Hela-S3	cervix:	n/a	n/a
39	USF1	chr7:99760670-99761127	A549	lung:	n/a	chr7:99760870-99760881
40	ATF3	chr7:99760729-99760978	K562	blood:	n/a	n/a
41	CHD2	chr7:99760749-99761065	Hela-S3	cervix:	n/a	n/a
42	MYC	chr7:99760736-99761040	MCF-7	breast:	n/a	chr7:99760870-99760883 chr7:99760870-99760883 chr7:99760872-99760881

No.	Distal block	Cell Line	Cell type
1	chr7:99759410..99761254-chr7:99763646..99766168,2	MCF-7	breast:
2	chr7:99758106..99763245-chr7:99767736..99770623,4	K562	blood:
3	chr7:99760302..99763071-chr7:99770976..99773286,2	K562	blood:
4	chr7:99688297..99690647-chr7:99759308..99762141,2	K562	blood:
5	chr7:99759295..99762077-chr7:100025040..100029116,3	MCF-7	breast:
6	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:
7	chr7:99758919..99761962-chr7:99764565..99766487,3	K562	blood:
8	chr7:99759440..99762424-chr7:99762477..99764332,2	K562	blood:
9	chr7:99754767..99758198-chr7:99759049..99763228,6	MCF-7	breast:
10	chr7:99760958..99763450-chr7:99810400..99812602,2	K562	blood:
11	chr7:99760942..99762936-chr7:99767762..99771413,3	MCF-7	breast:

Variant related genes	Relation type
C7orf43	TF binding region
ENSG00000197093	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000213420	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10231604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11764584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11771167	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878	0.83[YRI][hapmap]
rs1527423	0.89[CEU][hapmap]
rs1918352	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1918353	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2272337	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35042434	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736591	0.83[YRI][hapmap]
rs3779047	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3800951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807479	0.80[YRI][hapmap]
rs3823646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7785392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7787294	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs999885	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' 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	1132 gene(s)	inside rSNPs	diseases
2	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv888773	chr7:99751594-99772298	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv971181	chr7:99757433-99769748	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2405440	ZKSCAN1	cis	multi-tissue	Pritchard
rs2405440	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs2405440	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs2405440	AP4M1	cis	Artery Tibial	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99756600-99764200	Weak transcription	Spleen	Spleen
2	chr7:99756800-99764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99756800-99765200	Weak transcription	Right Atrium	heart
4	chr7:99756800-99765400	Weak transcription	Pancreas	Pancrea
5	chr7:99757000-99761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:99757000-99763800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:99757000-99763800	Weak transcription	Fetal Brain Female	brain
8	chr7:99757000-99764000	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:99757000-99764000	Weak transcription	Fetal Lung	lung
10	chr7:99757000-99764600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:99757000-99764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:99757000-99765000	Weak transcription	HSMM	muscle
13	chr7:99757000-99765400	Weak transcription	HSMMtube	muscle
14	chr7:99757200-99761600	Weak transcription	Esophagus	oesophagus
15	chr7:99757200-99764000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:99757200-99764800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:99758400-99761400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:99759400-99761600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:99759400-99763000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr7:99759600-99761800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:99759600-99763600	Genic enhancers	Fetal Thymus	thymus
22	chr7:99759800-99762400	Enhancers	Placenta	Placenta
23	chr7:99760200-99762000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:99760400-99761000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:99760400-99761200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr7:99760400-99761200	Enhancers	Fetal Intestine Large	intestine
27	chr7:99760400-99761400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr7:99760400-99761600	Enhancers	Fetal Intestine Small	intestine
29	chr7:99760400-99762000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:99760400-99762000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:99760400-99762200	Genic enhancers	Thymus	Thymus
32	chr7:99760400-99762400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr7:99760600-99761000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr7:99760600-99761000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:99760600-99761000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr7:99760600-99761000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr7:99760600-99761000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:99760600-99761000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr7:99760600-99761000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr7:99760600-99761000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:99760600-99761000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:99760600-99761000	Enhancers	Duodenum Mucosa	Duodenum
43	chr7:99760600-99761000	Flanking Active TSS	Hela-S3	cervix
44	chr7:99760600-99761200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr7:99760600-99761200	Enhancers	Colonic Mucosa	Colon
46	chr7:99760600-99761400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr7:99760600-99761400	Enhancers	Primary B cells from cord blood	blood
48	chr7:99760600-99761400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr7:99760600-99761400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:99760600-99761400	Enhancers	Placenta Amnion	Placenta Amnion

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