Variant report

Variant	rs35311230
Chromosome Location	chr15:43633497-43633498
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43625690..43629602-chr15:43629922..43634519,5	K562	blood:
2	chr15:43621044..43624825-chr15:43626235..43637209,16	K562	blood:
3	chr15:43632397..43634657-chr15:43658728..43661211,2	K562	blood:
4	chr15:43620805..43624764-chr15:43626235..43634573,14	K562	blood:
5	chr15:43620391..43624080-chr15:43631621..43634687,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10518812	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900259	0.84[AFR][1000 genomes]
rs12907870	0.83[AFR][1000 genomes]
rs12908460	0.83[AMR][1000 genomes]
rs12911569	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12911740	0.82[AFR][1000 genomes]
rs12913977	0.82[AFR][1000 genomes]
rs12914122	0.82[AFR][1000 genomes]
rs16957680	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16957715	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16957730	0.82[AFR][1000 genomes]
rs17723479	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17780417	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17780920	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1814324	0.85[EUR][1000 genomes]
rs2230451	0.83[AMR][1000 genomes]
rs34178146	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34181131	0.84[AFR][1000 genomes]
rs34515241	0.82[EUR][1000 genomes]
rs34591748	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34633582	0.81[AFR][1000 genomes]
rs34657657	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34661349	0.83[AFR][1000 genomes]
rs34697113	0.82[AFR][1000 genomes]
rs34715468	0.93[AFR][1000 genomes]
rs34767197	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34860428	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34921640	0.84[AFR][1000 genomes]
rs35158584	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35160541	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35278805	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326382	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35681736	0.85[EUR][1000 genomes]
rs35992154	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36078097	0.84[AFR][1000 genomes]
rs514438	0.85[EUR][1000 genomes]
rs55748552	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55801120	0.81[AFR][1000 genomes]
rs57728767	0.81[AFR][1000 genomes]
rs60018990	0.82[AFR][1000 genomes]
rs62019432	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019442	0.81[AFR][1000 genomes]
rs62020574	0.84[AFR][1000 genomes]
rs62021176	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62021180	0.83[AMR][1000 genomes]
rs66629206	0.82[AFR][1000 genomes]
rs71476435	0.81[AFR][1000 genomes]
rs7173383	0.82[AFR][1000 genomes]
rs7176923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7177892	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7180812	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7181545	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7181634	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7181783	0.82[AFR][1000 genomes]
rs7182292	0.84[AFR][1000 genomes]
rs7183708	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72707530	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72709850	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35311230	LCMT2	cis	Esophagus Mucosa	GTEx
rs35311230	TGM7	cis	Esophagus Mucosa	GTEx
rs35311230	ZSCAN29	cis	multi-tissue	Pritchard
rs35311230	ZSCAN29	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:43623200-43651000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
5	chr15:43623400-43639600	Weak transcription	Fetal Kidney	kidney
6	chr15:43623400-43641200	Weak transcription	Colonic Mucosa	Colon
7	chr15:43623400-43644000	Weak transcription	Fetal Thymus	thymus
8	chr15:43623400-43649200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
10	chr15:43623400-43651000	Weak transcription	Gastric	stomach
11	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
12	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:43623600-43637800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:43623600-43638000	Weak transcription	Fetal Brain Female	brain
15	chr15:43623600-43642600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:43623600-43642600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:43623600-43643200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:43623600-43644000	Weak transcription	Brain Germinal Matrix	brain
19	chr15:43623600-43644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:43623600-43646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:43623600-43646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:43623600-43646600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:43623600-43646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:43623600-43650400	Weak transcription	NH-A	brain
25	chr15:43623600-43650800	Weak transcription	HMEC	breast
26	chr15:43623600-43650800	Weak transcription	NHLF	lung
27	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:43623600-43651000	Weak transcription	A549	lung
29	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:43623800-43633800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:43623800-43638000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:43623800-43638200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:43623800-43641800	Weak transcription	Psoas Muscle	Psoas
34	chr15:43623800-43645800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:43623800-43646000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:43624000-43641200	Weak transcription	NHEK	skin
37	chr15:43624000-43647000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:43624600-43644600	Weak transcription	Fetal Heart	heart
39	chr15:43625600-43647200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:43625800-43636400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:43627000-43633600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr15:43627200-43633600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:43627200-43633600	Strong transcription	Liver	Liver
44	chr15:43627200-43636400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:43627600-43635200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:43627800-43633800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:43628000-43634200	Strong transcription	Fetal Intestine Large	intestine
48	chr15:43628200-43635800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:43628400-43650400	Weak transcription	Primary B cells from cord blood	blood
50	chr15:43628600-43633800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links