Variant report

Variant	rs35958032
Chromosome Location	chr15:43786595-43786596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43783239..43787260-chr15:43801022..43804758,8	K562	blood:
2	chr15:43780014..43781586-chr15:43785378..43787183,2	K562	blood:
3	chr15:43785564..43788713-chr15:43788914..43791066,4	K562	blood:
4	15:43785993-43792489..15:44080886-44089111	Hela-S3	cervix:
5	chr15:43784031..43792065-chr15:43801022..43804774,10	K562	blood:

Variant related genes	Relation type
ENSG00000140264	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000242028	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10518812	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899865	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12900259	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905220	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12906017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906481	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12907870	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12908460	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911569	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12911740	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12913977	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12914122	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16957680	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957715	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957730	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17723479	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17727853	0.82[AMR][1000 genomes]
rs17780417	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17780920	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814324	0.83[EUR][1000 genomes]
rs2230451	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34002293	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34178146	0.86[EUR][1000 genomes]
rs34181131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34212866	0.82[EUR][1000 genomes]
rs34388946	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34515241	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34591748	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34633582	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34657657	0.83[EUR][1000 genomes]
rs34661349	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34697113	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34767197	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34860428	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34921640	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35158584	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35160541	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35278805	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35326382	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35681736	0.83[EUR][1000 genomes]
rs35903301	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35975365	0.82[AMR][1000 genomes]
rs35992154	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36078097	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3862138	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs514438	0.84[EUR][1000 genomes]
rs55748552	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55801120	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56246169	0.82[AMR][1000 genomes]
rs57728767	0.92[EUR][1000 genomes]
rs57938858	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60018990	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60367691	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62019432	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62020574	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62020575	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62020612	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020616	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62021176	0.89[EUR][1000 genomes]
rs62021180	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476435	1.00[EUR][1000 genomes]
rs7173383	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7176923	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177146	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177892	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180812	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181545	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181634	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181783	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182292	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183708	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72707530	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709850	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709879	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027748	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8038068	0.82[AMR][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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35958032	LCMT2	cis	Esophagus Mucosa	GTEx
rs35958032	ZSCAN29	cis	multi-tissue	Pritchard
rs35958032	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs35958032	TGM7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43786000-43786600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr15:43786000-43786600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr15:43786000-43786600	Enhancers	Fetal Intestine Large	intestine
4	chr15:43786000-43786600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr15:43786000-43787200	Enhancers	Fetal Muscle Leg	muscle
6	chr15:43786000-43801800	Weak transcription	Primary T cells from cord blood	blood
7	chr15:43786200-43786600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr15:43786200-43786600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr15:43786200-43786600	Enhancers	Fetal Brain Female	brain
10	chr15:43786200-43786600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr15:43786200-43786600	Enhancers	K562	blood
12	chr15:43786200-43787400	Weak transcription	Placenta	Placenta
13	chr15:43786200-43788600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:43786200-43789000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:43786200-43789400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:43786200-43791200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:43786200-43792200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:43786200-43792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:43786200-43797400	Weak transcription	HSMM	muscle
20	chr15:43786200-43797800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:43786200-43798000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:43786200-43801200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:43786200-43801200	Weak transcription	Ovary	ovary
24	chr15:43786400-43786600	Enhancers	Brain Germinal Matrix	brain
25	chr15:43786400-43786600	Enhancers	HepG2	liver
26	chr15:43786400-43787000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:43786400-43798000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:43786400-43801000	Weak transcription	Dnd41	blood

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