Variant report

Variant	rs1557996
Chromosome Location	chr7:7657304-7657305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr7:7657217-7657508	K562	blood:	n/a	n/a
2	ARID3A	chr7:7656955-7657594	K562	blood:	n/a	n/a
3	STAT5A	chr7:7657143-7657518	K562	blood:	n/a	n/a
4	TBL1XR1	chr7:7657209-7657559	K562	blood:	n/a	n/a
5	MYC	chr7:7657252-7657496	K562	blood:	n/a	n/a
6	EP300	chr7:7656777-7657584	K562	blood:	n/a	chr7:7657256-7657270
7	IRF1	chr7:7657254-7657454	K562	blood:	n/a	n/a
8	ZNF384	chr7:7656643-7657632	K562	blood:	n/a	chr7:7657484-7657492
9	GATA1	chr7:7656870-7657732	PBDE	blood:	n/a	n/a
10	PML	chr7:7657135-7657546	K562	blood:	n/a	n/a
11	MYC	chr7:7657223-7657504	K562	blood:	n/a	n/a
12	EP300	chr7:7657259-7657329	GM12878	blood:	n/a	n/a
13	JUN	chr7:7657283-7657533	K562	blood:	n/a	n/a
14	IRF1	chr7:7656858-7657575	K562	blood:	n/a	n/a
15	IRF1	chr7:7656916-7657686	K562	blood:	n/a	n/a
16	ATF1	chr7:7657221-7657576	K562	blood:	n/a	n/a
17	JUND	chr7:7657225-7657537	K562	blood:	n/a	n/a
18	TEAD4	chr7:7657072-7657634	K562	blood:	n/a	n/a
19	TAL1	chr7:7657181-7657502	K562	blood:	n/a	n/a
20	RCOR1	chr7:7657226-7657563	K562	blood:	n/a	n/a
21	GATA3	chr7:7657295-7657587	SH-SY5Y	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:7617917..7620537-chr7:7654748..7657548,3	K562	blood:
2	chr7:7655938..7658869-chr7:7680457..7682421,2	K562	blood:
3	chr7:7650609..7654175-chr7:7655062..7657334,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272745	TF binding region
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10236714	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10250880	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11772656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13438316	1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs1548610	0.94[AFR][1000 genomes]
rs16878455	1.00[CHB][hapmap]
rs2051911	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079387	0.84[ASN][1000 genomes]
rs2108065	1.00[CHB][hapmap]
rs2158755	0.85[CEU][hapmap]
rs2881867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757528	1.00[CHB][hapmap]
rs3779375	1.00[CHB][hapmap]
rs3807857	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4725006	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463710	1.00[CHB][hapmap]
rs6948086	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6966601	1.00[CHB][hapmap]
rs7777893	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7781543	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7782245	1.00[CHB][hapmap]
rs7788388	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs7793675	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7801325	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1557996	MIOS	cis	cerebellum	SCAN
rs1557996	RPA3	cis	parietal	SCAN
rs1557996	MIOS	cis	parietal	SCAN
rs1557996	COL28A1	cis	cerebellum	SCAN
rs1557996	COL28A1	cis	parietal	SCAN
rs1557996	C16orf5	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7637600-7658000	Weak transcription	Fetal Intestine Small	intestine
2	chr7:7639800-7674600	Weak transcription	A549	lung
3	chr7:7647800-7657600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:7648600-7660200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:7649000-7679000	Weak transcription	HSMM	muscle
6	chr7:7649200-7657600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:7649800-7657800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr7:7656600-7657800	Enhancers	Primary T cells from cord blood	blood
9	chr7:7656800-7657400	Flanking Active TSS	K562	blood
10	chr7:7657200-7657400	Flanking Active TSS	Dnd41	blood
11	chr7:7657200-7657800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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