Variant report

Variant	rs3829897
Chromosome Location	chr7:50629764-50629765
allele	G/T
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	POLR2A	chr7:50629558-50630295	HepG2	liver:	n/a	n/a
2	MXI1	chr7:50624122-50630583	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr7:50629753-50630188	SK-N-SH_RA	brain:	n/a	chr7:50630171-50630184
4	RAD21	chr7:50625784-50630691	SK-N-SH	brain:	n/a	chr7:50629522-50629536 chr7:50627827-50627837 chr7:50630171-50630184 chr7:50628902-50628912
5	CTCF	chr7:50629700-50629850	BE2_C	brain:	n/a	n/a

Variant related genes	Relation type
DDC	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10229102	0.81[EUR][1000 genomes]
rs10229369	0.81[EUR][1000 genomes]
rs10238413	0.93[ASN][1000 genomes]
rs10247443	0.81[EUR][1000 genomes]
rs10250513	0.82[EUR][1000 genomes]
rs10274172	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10278338	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238214	0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11238226	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11489734	0.80[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11489736	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11974297	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs11977415	0.82[EUR][1000 genomes]
rs12665904	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12669770	0.83[EUR][1000 genomes]
rs1451373	0.82[EUR][1000 genomes]
rs1451374	0.82[EUR][1000 genomes]
rs1451375	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs17133878	0.86[EUR][1000 genomes]
rs1813214	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1839740	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1966839	0.84[EUR][1000 genomes]
rs1987859	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2329340	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs2329341	0.81[EUR][1000 genomes]
rs2329342	0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs4275187	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4392851	0.82[ASN][1000 genomes]
rs4452748	0.81[GIH][hapmap];0.83[EUR][1000 genomes]
rs4469404	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4512339	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4601266	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4947684	0.93[ASN][1000 genomes]
rs55738142	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56233242	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59086818	0.84[EUR][1000 genomes]
rs6593010	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68143668	0.83[EUR][1000 genomes]
rs6949897	0.82[EUR][1000 genomes]
rs6962356	0.81[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs6969081	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs73125288	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73125290	0.88[EUR][1000 genomes]
rs7797131	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7802148	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804365	0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs921450	0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs921451	0.81[GIH][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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 target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS 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 target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3829897	FIGNL1	cis	parietal	SCAN
rs3829897	FIGNL1	cis	Nerve Tibial	GTEx
rs3829897	FIGNL1	cis	cerebellum	SCAN
rs3829897	FIGNL1	cis	lung	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:50611000-50631800	Weak transcription	Colonic Mucosa	Colon
3	chr7:50620800-50635600	Weak transcription	Lung	lung
4	chr7:50624600-50631800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:50626800-50631800	Weak transcription	Gastric	stomach
6	chr7:50626800-50632000	Weak transcription	Stomach Mucosa	stomach
7	chr7:50627800-50631600	Enhancers	Liver	Liver
8	chr7:50628200-50630400	Enhancers	Pancreas	Pancrea
9	chr7:50628400-50629800	Weak transcription	Spleen	Spleen
10	chr7:50628600-50630000	Enhancers	Fetal Intestine Large	intestine
11	chr7:50628600-50630200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:50628600-50630400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr7:50628600-50632000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:50628800-50630400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:50629000-50629800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:50629200-50629800	Enhancers	HepG2	liver
17	chr7:50629200-50630000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:50629200-50632800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:50629400-50630800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr7:50629600-50629800	Enhancers	Fetal Kidney	kidney
21	chr7:50629600-50630000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:50629600-50630400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:50629600-50630800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine

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