Variant report

Variant	rs395358
Chromosome Location	chr6:88057924-88057925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs107689	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs107690	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1201409	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12190280	0.83[EUR][1000 genomes]
rs173333	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1753154	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs183599	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242267	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242270	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242278	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs242279	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs242280	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs242281	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs242283	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242285	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs242286	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs242287	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2474349	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2985039	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs369674	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs373646	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376633	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs381782	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3857488	0.81[EUR][1000 genomes]
rs390272	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445434	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs446851	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs447077	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs448580	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs451089	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs451465	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451829	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs586771	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454600	0.81[EUR][1000 genomes]
rs6921504	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs910563	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs395358	C6orf164	cis	Whole Blood	GTEx
rs395358	C6orf164	cis	Esophagus Muscularis	GTEx
rs395358	C6orf164	cis	Artery Tibial	GTEx
rs395358	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs395358	C6orf164	cis	lung	GTEx
rs395358	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs395358	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs395358	C6orf164	cis	Thyroid	GTEx
rs395358	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs395358	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88033200-88062200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:88039000-88068400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:88039000-88078400	Weak transcription	Fetal Stomach	stomach
4	chr6:88039400-88061200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:88040200-88075800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:88043600-88058400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:88043800-88061400	Weak transcription	Gastric	stomach
9	chr6:88043800-88068400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:88044000-88071400	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:88044400-88076000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:88044800-88072600	Weak transcription	Adipose Nuclei	Adipose
13	chr6:88044800-88075600	Weak transcription	Fetal Lung	lung
14	chr6:88045000-88059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:88048200-88059000	Weak transcription	Fetal Brain Female	brain
16	chr6:88049200-88066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:88049600-88061000	Weak transcription	Left Ventricle	heart
18	chr6:88050200-88062000	Weak transcription	Fetal Heart	heart
19	chr6:88050800-88060400	Weak transcription	Osteobl	bone
20	chr6:88051200-88071200	Weak transcription	Ovary	ovary
21	chr6:88051600-88070000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:88054200-88059000	Weak transcription	Psoas Muscle	Psoas
23	chr6:88054600-88067400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:88054600-88068400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:88054800-88075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
27	chr6:88055000-88063600	Weak transcription	HSMM	muscle
28	chr6:88055000-88075800	Weak transcription	Primary B cells from cord blood	blood
29	chr6:88055200-88072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:88057400-88073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:88057600-88077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links