Variant report

Variant	rs2472552
Chromosome Location	chr1:172527512-172527513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172501069..172504087-chr1:172524963..172528028,4	MCF-7	breast:
2	chr1:172418814..172420487-chr1:172526725..172528500,2	MCF-7	breast:
3	chr1:172524779..172527801-chr1:172528773..172532155,3	K562	blood:
4	chr1:172500883..172502906-chr1:172525690..172527673,2	MCF-7	breast:
5	chr1:172499469..172503029-chr1:172527261..172529453,3	K562	blood:
6	chr1:172500667..172503739-chr1:172526545..172530565,4	K562	blood:
7	chr1:172513266..172515531-chr1:172525208..172528046,2	K562	blood:

Variant related genes	Relation type
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10157519	0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10218613	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10489280	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10752994	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs10798040	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10911856	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912058	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912080	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912083	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10912084	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11805370	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12087284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12121051	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12146100	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1894625	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097492	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097493	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2097494	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097498	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2157420	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2227188	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2285144	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2422144	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472550	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2639621	0.81[EUR][1000 genomes]
rs3752515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768444	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4145436	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4433434	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5014539	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6424973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425007	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6656713	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6686080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686157	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695152	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525372	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7531652	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7539231	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539443	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs763108	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9425646	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9943276	0.82[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	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv872548	chr1:172518012-172551724	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2472552	SUCO	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
2	chr1:172503400-172528600	Weak transcription	Lung	lung
3	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
4	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
8	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:172511800-172528600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:172512000-172529000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:172512000-172534200	Weak transcription	Gastric	stomach
14	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
15	chr1:172514800-172528600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:172514800-172530200	Weak transcription	Thymus	Thymus
17	chr1:172515200-172528000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:172515200-172528200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:172515400-172528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:172516000-172532800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:172516200-172528800	Weak transcription	Pancreas	Pancrea
22	chr1:172516600-172528800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
24	chr1:172518000-172529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:172518600-172533000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:172519000-172530000	Weak transcription	NH-A	brain
27	chr1:172519000-172530200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:172519200-172528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:172519200-172529000	Weak transcription	Brain Germinal Matrix	brain
30	chr1:172519200-172534600	Weak transcription	Right Ventricle	heart
31	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
32	chr1:172519400-172527600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:172519400-172529000	Weak transcription	NHEK	skin
34	chr1:172519400-172533000	Weak transcription	HUVEC	blood vessel
35	chr1:172519400-172534600	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:172519400-172535400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:172519600-172528200	Weak transcription	GM12878-XiMat	blood
39	chr1:172519600-172528800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:172519600-172533000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:172519600-172533200	Weak transcription	Brain Anterior Caudate	brain
42	chr1:172519600-172538000	Weak transcription	Hela-S3	cervix
43	chr1:172519800-172534200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:172519800-172539200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:172521400-172532800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:172521800-172539800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:172521800-172540400	Strong transcription	Primary B cells from cord blood	blood
48	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:172522400-172528800	Weak transcription	Ovary	ovary
50	chr1:172523400-172531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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