Variant report

Variant	rs12073872
Chromosome Location	chr1:172550398-172550399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172548978..172551099-chr1:172556129..172558603,3	K562	blood:
2	chr1:172500935..172503676-chr1:172549899..172554092,3	MCF-7	breast:
3	chr1:172511443..172515146-chr1:172549683..172552996,3	K562	blood:
4	chr1:172528364..172530709-chr1:172549872..172552272,2	K562	blood:
5	chr1:172519187..172521470-chr1:172549104..172550723,2	K562	blood:
6	chr1:172549201..172550715-chr1:172556129..172558563,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10157501	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10752995	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911830	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs10911833	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10911843	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes]
rs10911859	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10911862	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10911875	0.84[ASN][1000 genomes]
rs10911920	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10912009	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912075	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1159378	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12021702	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12025433	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12038654	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041837	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070393	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093274	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12120798	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12123755	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130435	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12145007	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2239816	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2239817	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285143	0.80[ASN][1000 genomes]
rs2285664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2472549	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3738736	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754426	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3830150	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6424955	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs6424956	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6424965	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679222	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6688929	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs6691320	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6691528	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6699802	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs6702420	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs72710417	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514814	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517856	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7519911	0.91[ASN][1000 genomes]
rs7532580	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7542003	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553020	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9943237	0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs9970543	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs12073872	SUCO	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
3	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
4	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
5	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:172527000-172558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:172527800-172550400	Weak transcription	Stomach Mucosa	stomach
8	chr1:172527800-172554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:172534800-172558000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:172535200-172558000	Weak transcription	HSMMtube	muscle
11	chr1:172535400-172554200	Weak transcription	NHEK	skin
12	chr1:172535400-172558000	Weak transcription	Left Ventricle	heart
13	chr1:172535400-172558000	Weak transcription	Right Ventricle	heart
14	chr1:172535400-172558200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:172535600-172558000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:172535600-172569200	Weak transcription	Gastric	stomach
17	chr1:172536000-172558000	Weak transcription	Fetal Stomach	stomach
18	chr1:172536000-172565400	Weak transcription	Ovary	ovary
19	chr1:172536000-172565600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:172536000-172566000	Weak transcription	Aorta	Aorta
21	chr1:172537400-172565600	Weak transcription	Lung	lung
22	chr1:172539800-172550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:172540200-172550800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:172540200-172557400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:172540200-172558000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:172540200-172581000	Weak transcription	Colonic Mucosa	Colon
27	chr1:172540400-172550400	Weak transcription	NHLF	lung
28	chr1:172540400-172554200	Weak transcription	HMEC	breast
29	chr1:172540400-172555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:172540400-172557000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:172540400-172557800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:172540400-172557800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:172540400-172557800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:172540400-172557800	Weak transcription	Thymus	Thymus
35	chr1:172540400-172557800	Weak transcription	GM12878-XiMat	blood
36	chr1:172540400-172558000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:172540400-172558000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:172540400-172558000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:172540400-172558000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:172540400-172558000	Weak transcription	Fetal Brain Female	brain
41	chr1:172540400-172558000	Weak transcription	Fetal Kidney	kidney
42	chr1:172540400-172558000	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:172540400-172558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:172540400-172558400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:172540400-172559600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:172540400-172565600	Weak transcription	Esophagus	oesophagus
47	chr1:172540400-172565800	Weak transcription	Pancreas	Pancrea
48	chr1:172540600-172550600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:172540600-172565400	Weak transcription	Fetal Intestine Small	intestine
50	chr1:172541000-172555400	Weak transcription	H1 Cell Line	embryonic stem cell

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