Variant report

Variant	rs9874480
Chromosome Location	chr3:119139079-119139080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119137043..119139802-chr3:119141104..119143797,2	K562	blood:
2	chr3:119137603..119139843-chr3:119394787..119396303,2	MCF-7	breast:
3	chr3:119138626..119139712-chr3:119399725..119401267,5	MCF-7	breast:
4	chr3:119130788..119134912-chr3:119135156..119139620,7	K562	blood:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1060569	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13080905	0.98[ASN][1000 genomes]
rs1797839	0.86[ASN][1000 genomes]
rs1900742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919590	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976919	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2177812	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814397	0.86[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.98[ASN][1000 genomes]
rs4688005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688008	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688014	0.85[ASN][1000 genomes]
rs6414282	0.96[ASN][1000 genomes]
rs6414283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6778945	0.88[ASN][1000 genomes]
rs6794822	0.96[ASN][1000 genomes]
rs6796970	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7621259	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628626	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630587	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9809155	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836326	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850447	0.88[ASN][1000 genomes]
rs9867768	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs9873196	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9877854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
2	chr3:119110200-119140800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:119112000-119147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:119113200-119140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:119130200-119139200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:119130800-119143600	Weak transcription	GM12878-XiMat	blood
8	chr3:119133600-119140400	Weak transcription	NHLF	lung
9	chr3:119133800-119147400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
11	chr3:119134600-119147600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:119134800-119139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:119134800-119147400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:119135000-119139200	Weak transcription	Right Atrium	heart
15	chr3:119135000-119140800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:119135000-119147400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:119135000-119147600	Weak transcription	Fetal Thymus	thymus
18	chr3:119135000-119147800	Weak transcription	Placenta	Placenta
19	chr3:119135000-119148000	Weak transcription	Aorta	Aorta
20	chr3:119135200-119139200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:119135200-119139600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:119135200-119139800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:119135200-119140800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:119135200-119145000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:119135200-119149800	Weak transcription	Gastric	stomach
26	chr3:119135400-119145600	Weak transcription	HUVEC	blood vessel
27	chr3:119135400-119147800	Weak transcription	Ovary	ovary
28	chr3:119135400-119148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
30	chr3:119135600-119139200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:119136800-119145600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:119137000-119139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:119137000-119142000	Weak transcription	NH-A	brain
34	chr3:119137200-119141800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:119137400-119139400	Weak transcription	Primary T cells from cord blood	blood
36	chr3:119137400-119142200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:119137400-119145400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:119137400-119145400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:119137400-119147800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:119137600-119139200	Enhancers	K562	blood
41	chr3:119137600-119139600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:119137800-119146800	Weak transcription	Osteobl	bone
43	chr3:119138000-119140400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:119138000-119148400	Weak transcription	Fetal Stomach	stomach
45	chr3:119138000-119152400	Weak transcription	Lung	lung
46	chr3:119138200-119140200	Weak transcription	Adipose Nuclei	Adipose
47	chr3:119138200-119140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:119139000-119139200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:119139000-119139200	Flanking Active TSS	Fetal Heart	heart
50	chr3:119139000-119139400	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links