Variant report

Variant	rs17366234
Chromosome Location	chr3:136577085-136577086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136569165..136571514-chr3:136573850..136577535,3	K562	blood:
2	chr3:136568394..136571514-chr3:136574804..136577535,3	K562	blood:
3	chr3:136576539..136579211-chr3:136579578..136582893,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG1-1	chr3:136576895-136577445	NONHSAT092291

Variant related genes	Relation type
ENSG00000158092	Chromatin interaction
ENSG00000239213	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10935199	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486911	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1609391	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28458819	0.83[EUR][1000 genomes]
rs28877307	0.80[EUR][1000 genomes]
rs34799319	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4420814	0.81[EUR][1000 genomes]
rs4678441	0.85[EUR][1000 genomes]
rs4678442	0.85[EUR][1000 genomes]
rs56163507	0.80[EUR][1000 genomes]
rs56695781	0.81[EUR][1000 genomes]
rs60574021	0.83[EUR][1000 genomes]
rs67782618	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6793936	0.80[EUR][1000 genomes]
rs6802291	0.83[EUR][1000 genomes]
rs7621932	0.81[EUR][1000 genomes]
rs7633629	0.81[EUR][1000 genomes]
rs9757179	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136552600-136579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136554800-136578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:136554800-136579400	Weak transcription	Fetal Lung	lung
4	chr3:136555400-136579200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:136555600-136577800	Weak transcription	Lung	lung
6	chr3:136555600-136579200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:136555600-136580000	Weak transcription	Esophagus	oesophagus
8	chr3:136558200-136579200	Weak transcription	NHDF-Ad	bronchial
9	chr3:136558400-136579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:136558400-136579400	Weak transcription	Fetal Intestine Large	intestine
11	chr3:136558400-136579600	Weak transcription	NHEK	skin
12	chr3:136558600-136578000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:136558600-136578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:136558600-136578800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:136558600-136579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:136558600-136579200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:136558600-136579600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:136558600-136579600	Weak transcription	Liver	Liver
19	chr3:136558600-136579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:136558600-136579600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:136558600-136579800	Weak transcription	HSMM	muscle
22	chr3:136558800-136578600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:136558800-136578800	Weak transcription	HMEC	breast
24	chr3:136558800-136579000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:136558800-136579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:136558800-136579400	Weak transcription	Pancreas	Pancrea
27	chr3:136559000-136579400	Weak transcription	Brain Angular Gyrus	brain
28	chr3:136559000-136579600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:136559000-136580000	Weak transcription	Left Ventricle	heart
30	chr3:136559200-136579400	Weak transcription	Right Ventricle	heart
31	chr3:136559200-136579800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:136559600-136579400	Weak transcription	Placenta	Placenta
33	chr3:136559800-136579400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:136560200-136579200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:136561200-136579800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:136561400-136579400	Weak transcription	Fetal Kidney	kidney
37	chr3:136561800-136579400	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:136561800-136579400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:136563000-136579000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:136563000-136579200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:136565200-136579200	Weak transcription	Fetal Intestine Small	intestine
42	chr3:136565400-136578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:136565400-136578800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:136565600-136579000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:136565600-136579200	Weak transcription	Hela-S3	cervix
46	chr3:136565600-136579400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:136566800-136579400	Weak transcription	Psoas Muscle	Psoas
48	chr3:136567000-136579800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:136570000-136579600	Weak transcription	A549	lung
50	chr3:136571000-136579000	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links