Variant report

Variant	rs299088
Chromosome Location	chr5:68713660-68713661
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68713543-68713866	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68712271..68714793-chr7:7679143..7681371,2	MCF-7	breast:
2	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
3	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:

Variant related genes	Relation type
MARVELD2	TF binding region
ENSG00000197822	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000219545	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10035835	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10038816	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10044508	0.85[AFR][1000 genomes]
rs10064264	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10068576	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10077458	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10078100	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10471774	0.85[AFR][1000 genomes]
rs1168402	0.80[EUR][1000 genomes]
rs1168404	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1168405	0.80[EUR][1000 genomes]
rs1168407	0.80[EUR][1000 genomes]
rs1168409	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168410	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177556	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1183278	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1183879	0.81[EUR][1000 genomes]
rs1185246	0.81[EUR][1000 genomes]
rs182447	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2434507	0.81[EUR][1000 genomes]
rs2561159	0.80[EUR][1000 genomes]
rs2561160	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2561169	0.89[EUR][1000 genomes]
rs2561172	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2561186	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583699	0.81[EUR][1000 genomes]
rs28703034	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs299072	0.81[EUR][1000 genomes]
rs299073	0.81[EUR][1000 genomes]
rs299074	0.81[EUR][1000 genomes]
rs299075	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299077	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299078	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299086	0.81[EUR][1000 genomes]
rs299087	0.81[EUR][1000 genomes]
rs299090	0.81[EUR][1000 genomes]
rs299091	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299092	0.81[EUR][1000 genomes]
rs299093	0.81[EUR][1000 genomes]
rs299094	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299095	0.81[EUR][1000 genomes]
rs299098	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299099	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299101	0.80[EUR][1000 genomes]
rs299102	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4252228	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55747363	0.81[EUR][1000 genomes]
rs62373187	0.85[AFR][1000 genomes]
rs6450038	0.80[EUR][1000 genomes]
rs7712318	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs299088	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs299088	CCDC125	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68697800-68717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:68701200-68713800	Weak transcription	K562	blood
3	chr5:68711000-68713800	Weak transcription	HSMM	muscle
4	chr5:68711400-68716200	Weak transcription	Aorta	Aorta
5	chr5:68711400-68718200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:68711600-68715200	Weak transcription	NHLF	lung
7	chr5:68711600-68715400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:68711600-68715600	Weak transcription	Spleen	Spleen
9	chr5:68711600-68717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:68711600-68717400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:68711600-68722800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:68711600-68724000	Weak transcription	Right Atrium	heart
13	chr5:68711800-68715200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:68711800-68715200	Weak transcription	Lung	lung
15	chr5:68711800-68717200	Weak transcription	Osteobl	bone
16	chr5:68711800-68723600	Weak transcription	Small Intestine	intestine
17	chr5:68711800-68725000	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:68711800-68731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:68712000-68715600	Weak transcription	Primary T cells from cord blood	blood
20	chr5:68712000-68718800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:68712400-68714800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:68712400-68714800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:68712400-68715200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:68712400-68715200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:68712400-68715200	Weak transcription	Esophagus	oesophagus
26	chr5:68712400-68715200	Weak transcription	Placenta	Placenta
27	chr5:68712400-68715200	Weak transcription	Fetal Stomach	stomach
28	chr5:68712400-68715200	Weak transcription	Gastric	stomach
29	chr5:68712400-68715600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:68712400-68715600	Weak transcription	Fetal Lung	lung
31	chr5:68712400-68715600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:68712400-68715800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:68712400-68717200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:68712400-68719200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:68712400-68719400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:68712400-68731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:68712400-68735600	Weak transcription	Hela-S3	cervix
38	chr5:68712400-68739000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:68712400-68740400	Weak transcription	Fetal Kidney	kidney
40	chr5:68712600-68714800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:68712600-68715600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:68712600-68718400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:68712800-68714800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:68712800-68715000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr5:68712800-68715200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr5:68712800-68715200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:68712800-68738200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:68713000-68714000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr5:68713000-68714600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:68713000-68714800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links