Variant report

Variant	rs6973913
Chromosome Location	chr7:100662969-100662970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10229453	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs11766125	0.90[CHB][hapmap]
rs12532750	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs12538004	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs12539994	0.84[EUR][1000 genomes]
rs12540832	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs13231099	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13242391	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28441585	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34547547	0.80[ASN][1000 genomes]
rs3924886	0.90[CHB][hapmap]
rs4515470	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs55869514	0.81[ASN][1000 genomes]
rs56213152	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7806980	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1836983	chr7:100630638-100669857	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription 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 target site	39 gene(s)	inside rSNPs	diseases
13	esv1849981	chr7:100633668-100686761	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv1828583	chr7:100652181-100676353	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv1823966	chr7:100652181-100693849	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv3352938	chr7:100659732-100663130	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6973913	ZNF498	cis	parietal	SCAN
rs6973913	SERPINE1	cis	cerebellum	SCAN
rs6973913	SERPINE1	cis	parietal	SCAN
rs6973913	TRIM56	cis	parietal	SCAN
rs6973913	PILRB	cis	parietal	SCAN
rs6973913	C7orf59	cis	cerebellum	SCAN
rs6973913	GATS	cis	parietal	SCAN
rs6973913	TRRAP	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100661000-100663200	Enhancers	Fetal Intestine Large	intestine
2	chr7:100661000-100663200	Enhancers	Fetal Intestine Small	intestine
3	chr7:100661000-100664600	Weak transcription	Spleen	Spleen
4	chr7:100661000-100676800	Weak transcription	Right Atrium	heart
5	chr7:100661000-100684200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:100661600-100663200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:100661600-100663200	Enhancers	Duodenum Mucosa	Duodenum
8	chr7:100661600-100663600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:100661800-100663800	Enhancers	Stomach Mucosa	stomach
10	chr7:100662000-100663800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr7:100662200-100663000	Enhancers	GM12878-XiMat	blood
12	chr7:100662400-100664000	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:100662600-100665200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:100662800-100663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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