Variant report

Variant	rs12629658
Chromosome Location	chr3:101356535-101356536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101354125..101359417-chr3:101402279..101407297,7	K562	blood:
2	chr3:101290462..101294650-chr3:101353869..101359325,5	MCF-7	breast:
3	chr3:101279160..101282179-chr3:101355141..101357890,3	MCF-7	breast:
4	chr3:101354125..101356574-chr3:101403705..101405900,2	K562	blood:
5	chr3:101290829..101293797-chr3:101356493..101360609,3	K562	blood:

Variant related genes	Relation type
ENSG00000081154	Chromatin interaction
ENSG00000174173	Chromatin interaction
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1031710	0.85[EUR][1000 genomes]
rs1056579	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10936707	0.81[ASN][1000 genomes]
rs1138818	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes]
rs11708845	0.81[ASN][1000 genomes]
rs11710533	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711079	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712748	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714278	0.80[EUR][1000 genomes]
rs11715368	0.88[ASN][1000 genomes]
rs11717046	0.85[EUR][1000 genomes]
rs11720560	0.86[ASN][1000 genomes]
rs11720745	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11914318	0.86[EUR][1000 genomes]
rs11917569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11919389	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11923273	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11924013	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11925001	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635128	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12639028	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13059470	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061565	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069443	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077703	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081846	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13082236	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13100262	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17345786	0.84[ASN][1000 genomes]
rs17411983	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17508319	0.84[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes]
rs2288272	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2303474	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094295	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094296	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094297	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3109756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34301719	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34624546	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34883763	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35117343	0.87[EUR][1000 genomes]
rs35850993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36002990	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36060163	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762729	0.81[ASN][1000 genomes]
rs3804775	0.81[ASN][1000 genomes]
rs3806653	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806654	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3864012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55654108	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55821257	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56291106	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58907984	0.81[ASN][1000 genomes]
rs59596156	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62282218	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62282255	0.81[AFR][1000 genomes]
rs62284162	0.81[EUR][1000 genomes]
rs71625262	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73863360	0.84[ASN][1000 genomes]
rs7629753	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645391	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651406	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651721	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9830943	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs997739	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv992869	chr3:101348433-101360316	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv511216	chr3:101349644-101366921	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv3437268	chr3:101355562-101360160	Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12629658	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs12629658	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101350600-101366800	Weak transcription	Fetal Brain Female	brain
2	chr3:101354000-101356800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:101354200-101356600	Active TSS	K562	blood
4	chr3:101354200-101357000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:101354800-101366800	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:101355000-101356800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:101355000-101366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:101355200-101356600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:101355200-101356800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:101355200-101357000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:101355200-101357000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:101355200-101363000	Weak transcription	Fetal Thymus	thymus
13	chr3:101355200-101365000	Weak transcription	Right Atrium	heart
14	chr3:101355200-101367400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:101355200-101367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:101355600-101356600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:101355600-101357000	Weak transcription	HepG2	liver
18	chr3:101355600-101366400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:101355600-101366600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:101355600-101366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:101355600-101366600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:101355600-101367000	Weak transcription	A549	lung
23	chr3:101355600-101367000	Weak transcription	Dnd41	blood
24	chr3:101355600-101367400	Weak transcription	Right Ventricle	heart
25	chr3:101355600-101368600	Weak transcription	GM12878-XiMat	blood
26	chr3:101355800-101356600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:101356000-101367400	Weak transcription	Aorta	Aorta
28	chr3:101356400-101357400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:101356400-101357400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:101356400-101357600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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