Variant report

Variant	rs17110179
Chromosome Location	chr1:94091616-94091617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94090065..94091914-chr1:94120278..94122709,2	K562	blood:
2	chr1:94089082..94091665-chr1:94278876..94280669,2	MCF-7	breast:
3	chr1:94091548..94098915-chr1:94308687..94313875,7	K562	blood:
4	chr1:94080816..94083593-chr1:94090826..94092537,2	K562	blood:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11579004	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11580965	0.87[AMR][1000 genomes]
rs11588860	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739747	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12757325	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12760092	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12760246	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17110225	0.85[AMR][1000 genomes]
rs1877603	0.85[AMR][1000 genomes]
rs1877604	0.85[AMR][1000 genomes]
rs34183660	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34663884	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35126293	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59996315	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61780979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61780999	0.85[AMR][1000 genomes]
rs6679609	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6683296	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71652539	0.85[AMR][1000 genomes]
rs7553185	0.83[AMR][1000 genomes];0.96[EUR][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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17110179	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94081200-94095000	Genic enhancers	HSMM	muscle
4	chr1:94083400-94093800	Weak transcription	Psoas Muscle	Psoas
5	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
6	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:94083800-94095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:94085200-94092200	Enhancers	Placenta	Placenta
10	chr1:94085400-94093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:94085400-94107600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:94085800-94091800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:94086200-94092600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:94086800-94098000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:94086800-94101200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:94087400-94092600	Genic enhancers	Hela-S3	cervix
17	chr1:94087800-94092200	Enhancers	NHLF	lung
18	chr1:94088000-94091800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:94088000-94092400	Enhancers	NH-A	brain
20	chr1:94088200-94094800	Genic enhancers	A549	lung
21	chr1:94088200-94095600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:94088400-94092400	Weak transcription	Fetal Intestine Small	intestine
23	chr1:94088400-94093200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:94088400-94096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:94088400-94100400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:94088600-94091800	Weak transcription	Fetal Intestine Large	intestine
27	chr1:94088600-94118800	Weak transcription	Gastric	stomach
28	chr1:94089000-94092400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:94089400-94092400	Enhancers	NHDF-Ad	bronchial
30	chr1:94089400-94094000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:94089600-94092200	Enhancers	Left Ventricle	heart
32	chr1:94089600-94092200	Enhancers	HMEC	breast
33	chr1:94089600-94093000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:94089600-94097400	Genic enhancers	NHEK	skin
35	chr1:94089800-94092200	Enhancers	Right Atrium	heart
36	chr1:94090000-94093000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:94090000-94093000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:94090000-94095000	Weak transcription	Stomach Mucosa	stomach
39	chr1:94090200-94092600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:94090400-94092200	Enhancers	Osteobl	bone
41	chr1:94090400-94093800	Weak transcription	Lung	lung
42	chr1:94090400-94101400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:94090600-94101400	Weak transcription	Right Ventricle	heart
44	chr1:94090800-94091800	Enhancers	Fetal Lung	lung
45	chr1:94090800-94092200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:94090800-94092400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr1:94091000-94091800	Enhancers	Adipose Nuclei	Adipose
48	chr1:94091000-94091800	Enhancers	Brain Anterior Caudate	brain
49	chr1:94091000-94092200	Enhancers	Brain Hippocampus Middle	brain
50	chr1:94091000-94092600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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