Variant report

Variant	rs12635128
Chromosome Location	chr3:101360587-101360588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101359985..101362723-chr3:101395223..101396875,2	K562	blood:
2	chr3:101360573..101363913-chr3:101365432..101368273,3	K562	blood:
3	chr3:101290829..101293797-chr3:101356493..101360609,3	K562	blood:

Variant related genes	Relation type
ENSG00000201511	Chromatin interaction
ENSG00000256628	Chromatin interaction
ENSG00000066422	Chromatin interaction
ENSG00000081154	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];0.83[ASN][1000 genomes]
rs1056579	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1138818	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710533	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711079	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712748	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714278	0.80[EUR][1000 genomes]
rs11715368	0.82[ASN][1000 genomes]
rs11717046	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720560	0.81[ASN][1000 genomes]
rs11720745	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11914318	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11917569	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11917682	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11919389	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11923273	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11924013	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11925001	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12629658	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12636557	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639028	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059470	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13061565	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13066768	0.81[ASN][1000 genomes]
rs13069443	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13077703	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077925	0.81[ASN][1000 genomes]
rs13081846	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082236	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13099674	0.81[ASN][1000 genomes]
rs13100262	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17411983	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1963962	0.81[ASN][1000 genomes]
rs2288272	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303474	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2318090	0.81[ASN][1000 genomes]
rs3094295	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094296	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094297	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3109756	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181125	0.81[ASN][1000 genomes]
rs34301719	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34376498	0.81[ASN][1000 genomes]
rs34624546	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34883763	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35117343	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35850993	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36002990	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36060163	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806653	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3806654	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3864012	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55654108	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55821257	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55859364	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56291106	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59596156	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62282218	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62282255	0.82[AFR][1000 genomes]
rs62284162	0.81[EUR][1000 genomes]
rs62284198	0.81[ASN][1000 genomes]
rs62284199	0.81[ASN][1000 genomes]
rs71625262	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7629753	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645391	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7651406	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651721	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830943	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	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
3	esv3463450	chr3:101356762-101361660	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv591186	chr3:101358261-101362589	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12635128	NXPE3	cis	Esophagus Muscularis	GTEx
rs12635128	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101350600-101366800	Weak transcription	Fetal Brain Female	brain
2	chr3:101354800-101366800	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:101355000-101366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:101355200-101363000	Weak transcription	Fetal Thymus	thymus
5	chr3:101355200-101365000	Weak transcription	Right Atrium	heart
6	chr3:101355200-101367400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:101355200-101367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:101355600-101366400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:101355600-101366600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:101355600-101366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:101355600-101366600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:101355600-101367000	Weak transcription	A549	lung
13	chr3:101355600-101367000	Weak transcription	Dnd41	blood
14	chr3:101355600-101367400	Weak transcription	Right Ventricle	heart
15	chr3:101355600-101368600	Weak transcription	GM12878-XiMat	blood
16	chr3:101356000-101367400	Weak transcription	Aorta	Aorta
17	chr3:101356800-101362400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:101357400-101361400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:101357400-101362000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:101357400-101362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:101357400-101362200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:101357400-101362400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:101357400-101366600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:101357400-101367400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:101357600-101360800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:101357600-101362000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:101357600-101362200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:101357800-101362000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:101357800-101362000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:101357800-101362000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:101357800-101365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:101357800-101369400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:101358000-101362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:101359200-101362600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:101359800-101361400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:101359800-101363200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:101360200-101360800	Enhancers	K562	blood

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