Variant report

Variant	rs17480087
Chromosome Location	chr1:223494497-223494498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223306747..223308413-chr1:223494380..223496963,2	MCF-7	breast:
2	chr1:223482509..223485104-chr1:223493881..223496147,2	K562	blood:
3	chr1:223473310..223474999-chr1:223493022..223494928,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10495206	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10907376	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1115114	0.91[AFR][1000 genomes]
rs11261264	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11261270	0.91[AFR][1000 genomes]
rs12123148	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12140453	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12564615	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1341988	0.82[JPT][hapmap]
rs1400959	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400963	0.82[JPT][hapmap]
rs1418150	0.82[JPT][hapmap]
rs1547788	0.81[EUR][1000 genomes]
rs1640849	0.82[JPT][hapmap]
rs17162008	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17162072	0.84[JPT][hapmap]
rs17163827	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17163831	0.80[EUR][1000 genomes]
rs17479856	0.91[JPT][hapmap]
rs17480344	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17518349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17538964	0.91[JPT][hapmap]
rs17539269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17539583	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17577742	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17578168	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17578203	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1772280	0.83[EUR][1000 genomes]
rs34150324	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61838208	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61838209	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61838210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838230	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838231	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838234	0.81[EUR][1000 genomes]
rs61838235	0.81[EUR][1000 genomes]
rs61838238	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838239	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838240	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61838243	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61838250	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61838252	0.83[EUR][1000 genomes]
rs61839867	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7536652	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7541162	0.81[EUR][1000 genomes]
rs9442042	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17480087	SUSD4	cis	cerebellum	SCAN
rs17480087	SUSD4	cis	Heart Left Ventricle	GTEx
rs17480087	SUSD4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223487200-223496000	Weak transcription	Ovary	ovary
2	chr1:223489800-223495600	Weak transcription	Primary T cells from cord blood	blood
3	chr1:223492200-223497000	Weak transcription	Right Atrium	heart
4	chr1:223492400-223496200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:223492800-223494600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:223492800-223494800	Enhancers	Fetal Thymus	thymus
7	chr1:223493200-223494600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:223493200-223494600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223493200-223494600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:223493200-223494600	Enhancers	Esophagus	oesophagus
11	chr1:223493400-223496200	Weak transcription	Pancreas	Pancrea
12	chr1:223493600-223494600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:223493800-223494600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:223494200-223495600	Weak transcription	Thymus	Thymus
15	chr1:223494200-223496200	Weak transcription	Primary T cells fromperipheralblood	blood

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