Variant report

Variant	rs6424973
Chromosome Location	chr1:172546020-172546021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172417853..172420301-chr1:172543266..172546052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180999	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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10157519	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10218613	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10489280	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10752994	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs10798040	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10911856	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912058	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912080	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912083	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912084	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11805370	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12087284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12121051	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12146100	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1894625	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894626	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2097492	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097493	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097494	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2097498	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2157420	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2227188	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285144	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2422144	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2472550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472552	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]
rs2639621	0.84[EUR][1000 genomes]
rs3752515	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4145436	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4433434	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5014539	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425007	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656713	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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];0.92[ASN][1000 genomes]
rs6686157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695152	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7525372	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7531652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7539231	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539443	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs763108	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425646	1.00[CHB][hapmap];1.00[JPT][hapmap];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	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
2	esv3409125	chr1:172545981-172546200	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6424973	SUCO	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 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	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
4	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
5	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:172527000-172558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:172527800-172550400	Weak transcription	Stomach Mucosa	stomach
9	chr1:172527800-172554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:172528400-172547800	Weak transcription	A549	lung
11	chr1:172534800-172558000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:172535200-172547800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:172535200-172558000	Weak transcription	HSMMtube	muscle
14	chr1:172535400-172554200	Weak transcription	NHEK	skin
15	chr1:172535400-172558000	Weak transcription	Left Ventricle	heart
16	chr1:172535400-172558000	Weak transcription	Right Ventricle	heart
17	chr1:172535400-172558200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:172535600-172546400	Weak transcription	HepG2	liver
19	chr1:172535600-172558000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:172535600-172569200	Weak transcription	Gastric	stomach
21	chr1:172536000-172558000	Weak transcription	Fetal Stomach	stomach
22	chr1:172536000-172565400	Weak transcription	Ovary	ovary
23	chr1:172536000-172565600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:172536000-172566000	Weak transcription	Aorta	Aorta
25	chr1:172537400-172565600	Weak transcription	Lung	lung
26	chr1:172538800-172547600	Weak transcription	Hela-S3	cervix
27	chr1:172539800-172550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:172540200-172547400	Weak transcription	Fetal Brain Male	brain
29	chr1:172540200-172548200	Weak transcription	NHDF-Ad	bronchial
30	chr1:172540200-172550800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:172540200-172557400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:172540200-172558000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:172540200-172581000	Weak transcription	Colonic Mucosa	Colon
34	chr1:172540400-172546600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:172540400-172546600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:172540400-172547200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:172540400-172547200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:172540400-172547200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:172540400-172547200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:172540400-172547400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:172540400-172547600	Weak transcription	HUVEC	blood vessel
42	chr1:172540400-172547800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:172540400-172547800	Weak transcription	Brain Anterior Caudate	brain
44	chr1:172540400-172548600	Weak transcription	Adipose Nuclei	Adipose
45	chr1:172540400-172550200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:172540400-172550400	Weak transcription	NHLF	lung
47	chr1:172540400-172554200	Weak transcription	HMEC	breast
48	chr1:172540400-172555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:172540400-172557000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:172540400-172557800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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