Variant report

Variant	rs7485355
Chromosome Location	chr12:48548342-48548343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48496998..48499694-chr12:48547936..48550832,3	K562	blood:
2	chr12:48511519..48514886-chr12:48548320..48552889,5	K562	blood:
3	chr12:48545842..48549323-chr12:48549562..48552963,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10082861	0.94[ASN][1000 genomes]
rs10219623	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10219645	0.91[ASN][1000 genomes]
rs10875735	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875736	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875737	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10875738	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875740	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875745	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875746	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875747	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875748	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875756	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875762	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168383	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168386	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168401	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168403	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168413	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11168414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168415	0.95[ASN][1000 genomes]
rs11168416	0.95[ASN][1000 genomes]
rs11168418	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168420	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168421	0.94[ASN][1000 genomes]
rs11168422	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168425	0.97[ASN][1000 genomes]
rs11168427	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168433	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11558768	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12297004	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12297470	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12301339	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12304476	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12305511	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12305647	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12306290	0.92[ASN][1000 genomes]
rs12306451	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12310813	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12311774	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12311953	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12312134	0.92[ASN][1000 genomes]
rs12313300	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12313404	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12315625	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17122620	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17122666	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1859445	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2107638	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2158516	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2228500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269933	0.95[ASN][1000 genomes]
rs2269935	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286021	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782910	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3782911	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4760619	0.91[ASN][1000 genomes]
rs4760622	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760680	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760681	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760684	0.95[ASN][1000 genomes]
rs4760687	0.89[ASN][1000 genomes]
rs4760689	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760690	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760695	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58952582	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60106007	0.95[ASN][1000 genomes]
rs60761335	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61343568	0.89[ASN][1000 genomes]
rs61918806	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61918809	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61918810	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs725454	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73102065	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73102067	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7486424	0.89[ASN][1000 genomes]
rs8804	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886588	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs989144	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7485355	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs7485355	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs7485355	RP1-228P16.1	cis	Thyroid	GTEx
rs7485355	RP1-228P16.1	cis	Artery Tibial	GTEx
rs7485355	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48532200-48548400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48533600-48548400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:48536800-48550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48537800-48550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:48538400-48550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:48538600-48548600	Strong transcription	Thymus	Thymus
7	chr12:48540400-48550000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:48540400-48550200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:48542200-48550400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48543800-48550400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:48544000-48550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:48544000-48550200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48544000-48550400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48544000-48550400	Weak transcription	Esophagus	oesophagus
15	chr12:48544000-48550600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48544200-48550400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:48544400-48550000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:48544400-48550400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:48544600-48550400	Weak transcription	Stomach Mucosa	stomach
20	chr12:48544800-48550200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:48545000-48550200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:48545200-48550000	Weak transcription	HUVEC	blood vessel
23	chr12:48545200-48550200	Weak transcription	Small Intestine	intestine
24	chr12:48545400-48550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:48545400-48550200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:48545400-48550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:48545400-48550200	Weak transcription	Fetal Heart	heart
28	chr12:48545600-48549600	Weak transcription	Pancreas	Pancrea
29	chr12:48545600-48550000	Weak transcription	Fetal Brain Male	brain
30	chr12:48545600-48550200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:48545600-48550200	Weak transcription	NHEK	skin
32	chr12:48545600-48550200	Weak transcription	NHLF	lung
33	chr12:48545600-48550400	Weak transcription	Aorta	Aorta
34	chr12:48545800-48550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:48546200-48550000	Weak transcription	A549	lung
36	chr12:48546200-48550200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:48546200-48550200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:48546200-48550200	Weak transcription	Right Ventricle	heart
39	chr12:48546200-48550600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:48546400-48550000	Weak transcription	HepG2	liver
41	chr12:48546600-48549600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:48546800-48550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:48547000-48550200	Weak transcription	Fetal Kidney	kidney
44	chr12:48547200-48550000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:48547200-48550000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:48547200-48550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:48547200-48550000	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:48547200-48550000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:48547200-48550000	Weak transcription	NH-A	brain
50	chr12:48547200-48550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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