Variant report

Variant	rs1991431
Chromosome Location	chr3:141133450-141133451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141127732..141130108-chr3:141132601..141134481,2	MCF-7	breast:
2	chr3:141085385..141089817-chr3:141128434..141134875,8	K562	blood:
3	chr3:141133198..141135160-chr3:141173942..141176696,2	MCF-7	breast:
4	chr3:141118092..141121599-chr3:141132205..141135279,4	MCF-7	breast:
5	chr3:141029410..141031621-chr3:141132926..141134468,2	K562	blood:
6	chr3:141119704..141122794-chr3:141132983..141135901,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13068733	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13077048	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1344672	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1344674	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1346408	0.82[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863868	0.82[CEU][hapmap]
rs2114867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2871960	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683605	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4683606	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6440003	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6763927	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763931	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6764769	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6785012	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6808936	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724016	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs7625643	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7632381	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7650602	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9853018	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][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	23563607	GWAS catalog

Chromatin state (count:117 , 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	chr3:141129600-141133800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:141130200-141133600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr3:141130600-141133600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:141131200-141139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:141131400-141134200	Enhancers	Primary T cells from cord blood	blood
7	chr3:141131600-141133600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:141131600-141133600	Genic enhancers	Fetal Stomach	stomach
9	chr3:141131600-141134200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:141131600-141134400	Genic enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:141131600-141138800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:141131600-141144400	Strong transcription	Fetal Intestine Large	intestine
13	chr3:141131600-141145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:141131800-141133600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:141131800-141133600	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr3:141131800-141134000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:141131800-141134800	Genic enhancers	Osteobl	bone
18	chr3:141131800-141135600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:141131800-141136200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:141131800-141136200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:141131800-141136200	Genic enhancers	Lung	lung
22	chr3:141131800-141144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
24	chr3:141132000-141133600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr3:141132000-141133800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:141132000-141134600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:141132000-141137400	Genic enhancers	Left Ventricle	heart
28	chr3:141132200-141133800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:141132200-141133800	Weak transcription	Esophagus	oesophagus
30	chr3:141132200-141133800	Genic enhancers	HMEC	breast
31	chr3:141132200-141133800	Genic enhancers	NHEK	skin
32	chr3:141132200-141134000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:141132200-141134000	Genic enhancers	GM12878-XiMat	blood
34	chr3:141132200-141134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:141132200-141134200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:141132200-141134200	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr3:141132200-141134200	Weak transcription	Ovary	ovary
38	chr3:141132200-141134400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:141132200-141134400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:141132200-141134400	Genic enhancers	NH-A	brain
41	chr3:141132200-141135000	Genic enhancers	Brain Hippocampus Middle	brain
42	chr3:141132200-141135400	Genic enhancers	Hela-S3	cervix
43	chr3:141132200-141135400	Genic enhancers	HUVEC	blood vessel
44	chr3:141132200-141135600	Enhancers	Right Atrium	heart
45	chr3:141132200-141135800	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr3:141132200-141135800	Genic enhancers	NHLF	lung
47	chr3:141132200-141136400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:141132200-141138000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:141132200-141138600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:141132200-141141000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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