Variant report

Variant	rs9825379
Chromosome Location	chr3:141137035-141137036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141119463..141121606-chr3:141135948..141138544,2	MCF-7	breast:
2	chr3:141119613..141122470-chr3:141135749..141139240,4	MCF-7	breast:
3	chr3:141085279..141086915-chr3:141134988..141137791,2	K562	blood:
4	chr3:141134135..141137819-chr3:141137972..141141592,4	K562	blood:
5	chr3:141133859..141137101-chr3:141144302..141145927,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10513137	1.00[ASW][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11919595	0.85[CEU][hapmap]
rs1344673	0.85[CEU][hapmap]
rs16851397	0.85[CEU][hapmap]
rs16851412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16851416	0.95[EUR][1000 genomes]
rs6762826	0.84[TSI][hapmap]
rs6764191	0.81[YRI][hapmap]
rs6776991	0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6792546	0.89[YRI][hapmap]
rs6801329	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs6802753	0.84[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845854	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs9858405	0.98[AFR][1000 genomes]
rs9869102	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs9876694	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20189936	GWAS catalog

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141126800-141138000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:141131200-141139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:141131600-141138800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:141131600-141144400	Strong transcription	Fetal Intestine Large	intestine
5	chr3:141131600-141145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:141131800-141144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
8	chr3:141132000-141137400	Genic enhancers	Left Ventricle	heart
9	chr3:141132200-141138000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:141132200-141138600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:141132200-141141000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:141132200-141144400	Strong transcription	Fetal Intestine Small	intestine
13	chr3:141132200-141144800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:141132200-141171000	Weak transcription	Primary B cells from cord blood	blood
15	chr3:141132400-141137600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:141132400-141139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:141132600-141139000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:141132600-141139200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:141132800-141137800	Strong transcription	HSMMtube	muscle
20	chr3:141132800-141138400	Strong transcription	HSMM	muscle
21	chr3:141133000-141139000	Genic enhancers	Right Ventricle	heart
22	chr3:141133200-141138400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:141133400-141138400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:141133600-141138200	Strong transcription	Fetal Stomach	stomach
25	chr3:141133600-141139000	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:141133600-141139200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:141133600-141140600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:141133800-141137200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:141133800-141140400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:141133800-141140600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:141133800-141158400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:141133800-141158400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:141134000-141138600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:141134000-141138800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:141134000-141138800	Weak transcription	Spleen	Spleen
36	chr3:141134000-141146800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:141134000-141161600	Weak transcription	Fetal Brain Male	brain
38	chr3:141134200-141137800	Strong transcription	HepG2	liver
39	chr3:141134200-141139000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:141134200-141139000	Weak transcription	Small Intestine	intestine
41	chr3:141134200-141145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:141134200-141161600	Weak transcription	Primary T cells from cord blood	blood
43	chr3:141134400-141138200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:141134400-141138400	Strong transcription	NH-A	brain
45	chr3:141134400-141139200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr3:141134400-141140600	Weak transcription	Esophagus	oesophagus
47	chr3:141134600-141137200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:141134600-141137200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:141134600-141137200	Strong transcription	Gastric	stomach
50	chr3:141134600-141137200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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