Variant report

Variant	rs2609355
Chromosome Location	chr1:223177574-223177575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223174781..223178345-chr1:223180899..223184230,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1048209	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2255147	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2609351	0.93[EUR][1000 genomes]
rs2609352	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609353	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789912	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789931	0.93[JPT][hapmap]
rs2789948	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789949	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789951	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789958	0.83[ASW][hapmap];0.80[JPT][hapmap];0.91[LWK][hapmap]
rs2789972	0.87[JPT][hapmap]
rs2971990	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs728006	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv917330	chr1:223141547-223225893	Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2609355	ESRRG	cis	parietal	SCAN
rs2609355	MOSC1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223163600-223179800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:223166200-223179400	Weak transcription	Small Intestine	intestine
3	chr1:223169000-223184000	Weak transcription	HSMM	muscle
4	chr1:223169000-223184200	Weak transcription	HSMMtube	muscle
5	chr1:223169000-223187600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:223170200-223177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:223170200-223177800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:223170200-223183000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:223170200-223184200	Weak transcription	NH-A	brain
10	chr1:223172000-223179800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:223173200-223177600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:223174200-223179000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:223174200-223180400	Weak transcription	Fetal Thymus	thymus
14	chr1:223175000-223177800	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:223175000-223178000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:223175000-223178000	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:223175000-223178200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:223175000-223179000	Strong transcription	Left Ventricle	heart
19	chr1:223175000-223180200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:223175200-223179400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:223175200-223184200	Weak transcription	Colonic Mucosa	Colon
22	chr1:223175200-223189800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:223175400-223178600	Strong transcription	Primary B cells from cord blood	blood
24	chr1:223175400-223180200	Strong transcription	Primary T cells from cord blood	blood
25	chr1:223175400-223180200	Weak transcription	NHDF-Ad	bronchial
26	chr1:223175600-223177600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:223175600-223177800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:223175600-223177800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:223175600-223177800	Strong transcription	Fetal Kidney	kidney
30	chr1:223175600-223178000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr1:223175600-223178000	Strong transcription	Thymus	Thymus
32	chr1:223175600-223178200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:223175600-223178400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr1:223175600-223178400	Strong transcription	Fetal Stomach	stomach
35	chr1:223175600-223178600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:223175600-223178600	Strong transcription	Liver	Liver
37	chr1:223175600-223178600	Strong transcription	Fetal Brain Female	brain
38	chr1:223175600-223178600	Strong transcription	Ovary	ovary
39	chr1:223175600-223178800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:223175600-223178800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:223175600-223178800	Strong transcription	Brain Hippocampus Middle	brain
42	chr1:223175600-223178800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:223175600-223178800	Strong transcription	Pancreas	Pancrea
44	chr1:223175600-223179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:223175600-223179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:223175600-223179000	Strong transcription	Fetal Intestine Small	intestine
47	chr1:223175600-223179000	Strong transcription	Right Ventricle	heart
48	chr1:223175600-223179200	Strong transcription	Lung	lung
49	chr1:223175600-223180000	Weak transcription	HepG2	liver
50	chr1:223175600-223180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links