Variant report

Variant	rs11588860
Chromosome Location	chr1:94094479-94094480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94092851..94096597-chr1:94146302..94147993,4	MCF-7	breast:
2	chr1:94093742..94096108-chr1:94309968..94312070,2	K562	blood:
3	chr1:94091548..94098915-chr1:94308687..94313875,7	K562	blood:
4	chr1:94092980..94095729-chr1:94311272..94313318,3	MCF-7	breast:
5	chr1:94093897..94096295-chr1:94277751..94279857,3	MCF-7	breast:

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

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	1.00[ASN][1000 genomes]
rs11579004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579685	1.00[ASN][1000 genomes]
rs11580965	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12066343	1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	1.00[ASN][1000 genomes]
rs12739747	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740779	1.00[ASN][1000 genomes]
rs12744941	1.00[ASN][1000 genomes]
rs12757325	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760092	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760246	0.84[EUR][1000 genomes]
rs17110063	1.00[ASN][1000 genomes]
rs17110101	1.00[ASN][1000 genomes]
rs17110111	1.00[ASN][1000 genomes]
rs17110179	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17110225	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1877604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34423897	1.00[ASN][1000 genomes]
rs34663884	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34666525	1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	1.00[ASN][1000 genomes]
rs3950119	1.00[ASN][1000 genomes]
rs59996315	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61780979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61780999	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683296	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66966060	1.00[ASN][1000 genomes]
rs67043929	1.00[ASN][1000 genomes]
rs67300695	1.00[ASN][1000 genomes]
rs67354439	1.00[ASN][1000 genomes]
rs67511232	1.00[ASN][1000 genomes]
rs71652539	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72721041	1.00[ASN][1000 genomes]
rs7511890	1.00[ASN][1000 genomes]
rs7525880	1.00[ASN][1000 genomes]
rs7531106	1.00[ASN][1000 genomes]
rs7543098	1.00[ASN][1000 genomes]
rs7543763	1.00[ASN][1000 genomes]
rs7553185	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555302	1.00[ASN][1000 genomes]
rs761802	1.00[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	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
rs11588860	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 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	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
5	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:94083800-94095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:94085400-94107600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:94086800-94098000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:94086800-94101200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:94088200-94094800	Genic enhancers	A549	lung
12	chr1:94088200-94095600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:94088400-94096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:94088400-94100400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:94088600-94118800	Weak transcription	Gastric	stomach
16	chr1:94089600-94097400	Genic enhancers	NHEK	skin
17	chr1:94090000-94095000	Weak transcription	Stomach Mucosa	stomach
18	chr1:94090400-94101400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:94090600-94101400	Weak transcription	Right Ventricle	heart
20	chr1:94091000-94095000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:94091200-94095600	Enhancers	HUVEC	blood vessel
22	chr1:94091400-94097000	Weak transcription	HepG2	liver
23	chr1:94091600-94094600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:94091600-94095200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:94091600-94101000	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:94091600-94101400	Weak transcription	Brain Angular Gyrus	brain
27	chr1:94091600-94106600	Weak transcription	Aorta	Aorta
28	chr1:94091600-94107600	Weak transcription	Ovary	ovary
29	chr1:94091800-94117400	Weak transcription	Fetal Lung	lung
30	chr1:94092000-94095200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:94092200-94095200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:94092200-94097000	Weak transcription	Placenta	Placenta
33	chr1:94092200-94097800	Genic enhancers	HMEC	breast
34	chr1:94092200-94100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:94092200-94101000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:94092400-94097000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:94093000-94095200	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:94093000-94095400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:94093000-94100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:94093200-94095200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:94093200-94096400	Weak transcription	Fetal Intestine Small	intestine
42	chr1:94093200-94100600	Weak transcription	Brain Substantia Nigra	brain
43	chr1:94093600-94094600	Genic enhancers	NHLF	lung
44	chr1:94093600-94095200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:94093600-94096000	Enhancers	Osteobl	bone
46	chr1:94093600-94096400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:94093600-94097800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:94093800-94095400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:94093800-94095600	Enhancers	NH-A	brain
50	chr1:94093800-94097800	Genic enhancers	Muscle Satellite Cultured Cells	--

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