Variant report

Variant	rs56262662
Chromosome Location	chr17:34101844-34101845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:34101546..34103557-chr17:34109356..34111620,2	MCF-7	breast:
2	chr17:34101120..34102648-chr17:34132276..34135170,2	MCF-7	breast:
3	chr17:34101663..34103354-chr17:34121215..34124196,2	MCF-7	breast:
4	chr17:34094026..34096970-chr17:34100464..34102783,3	K562	blood:
5	chr17:34098510..34102735-chr17:34135277..34138625,5	MCF-7	breast:
6	chr17:34100630..34103583-chr17:34107031..34108595,2	K562	blood:

Variant related genes	Relation type
ENSG00000129270	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000267578	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10451309	0.90[ASN][1000 genomes]
rs2242596	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2242597	0.89[EUR][1000 genomes]
rs2280786	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2280788	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2293789	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28914802	0.89[EUR][1000 genomes]
rs28914816	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28914817	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28914819	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3826454	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4251700	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4251704	0.86[ASN][1000 genomes]
rs4251710	0.86[ASN][1000 genomes]
rs4251739	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55680144	1.00[EUR][1000 genomes]
rs55781042	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55792948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799023	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55833673	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55846484	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55906604	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55915639	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55951822	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56029903	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56077005	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56111312	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56135703	1.00[AFR][1000 genomes]
rs56170514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181735	0.89[EUR][1000 genomes]
rs56221144	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56305516	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56347933	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56382694	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60040900	0.92[ASN][1000 genomes]
rs72483217	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9901469	0.90[ASN][1000 genomes]
rs9907320	0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56262662	GAS2L2	cis	Heart Left Ventricle	GTEx
rs56262662	GAS2L2	cis	Muscle Skeletal	GTEx
rs56262662	GAS2L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34091800-34103600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:34092400-34114200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr17:34097600-34102800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr17:34098800-34102400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:34098800-34102600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:34098800-34102800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr17:34098800-34102800	Enhancers	Primary hematopoietic stem cells	blood
8	chr17:34098800-34103600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:34099000-34102400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:34099400-34103000	Enhancers	Fetal Thymus	thymus
11	chr17:34100000-34102000	Enhancers	Right Ventricle	heart
12	chr17:34100000-34102600	Enhancers	Fetal Heart	heart
13	chr17:34100000-34102800	Enhancers	Fetal Lung	lung
14	chr17:34100000-34103000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr17:34100200-34102600	Enhancers	HSMMtube	muscle
16	chr17:34100200-34103000	Enhancers	Fetal Muscle Leg	muscle
17	chr17:34100400-34102200	Enhancers	Fetal Muscle Trunk	muscle
18	chr17:34100400-34102600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:34100400-34102600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:34100400-34102600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:34100400-34102600	Enhancers	Lung	lung
22	chr17:34100400-34104600	Enhancers	Stomach Mucosa	stomach
23	chr17:34100600-34102000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:34100600-34102000	Enhancers	Fetal Intestine Large	intestine
25	chr17:34100600-34102400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:34100600-34102400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:34100600-34102600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr17:34100600-34102600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr17:34100600-34102800	Enhancers	Brain Anterior Caudate	brain
30	chr17:34100600-34102800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:34100600-34102800	Enhancers	Fetal Intestine Small	intestine
32	chr17:34100600-34102800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr17:34100600-34102800	Enhancers	Right Atrium	heart
34	chr17:34100600-34103200	Enhancers	Duodenum Mucosa	Duodenum
35	chr17:34100800-34102000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr17:34100800-34102200	Enhancers	Placenta	Placenta
37	chr17:34100800-34102200	Enhancers	HSMM	muscle
38	chr17:34100800-34102200	Enhancers	Osteobl	bone
39	chr17:34100800-34102400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:34100800-34102800	Enhancers	Colonic Mucosa	Colon
41	chr17:34100800-34102800	Enhancers	Fetal Brain Male	brain
42	chr17:34100800-34102800	Enhancers	Hela-S3	cervix
43	chr17:34101000-34102000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr17:34101000-34102000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr17:34101000-34102400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:34101000-34102600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr17:34101000-34102600	Enhancers	NH-A	brain
48	chr17:34101000-34102800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr17:34101000-34102800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr17:34101200-34102000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links