Variant report

Variant	rs2060271
Chromosome Location	chr19:39952006-39952007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39948878..39954067-chr19:39954959..39958425,6	K562	blood:
2	chr19:39950586..39952165-chr19:39983591..39985551,2	K562	blood:
3	chr19:39950484..39953457-chr19:39955468..39957476,3	K562	blood:
4	chr19:39947684..39949620-chr19:39951964..39953477,2	K562	blood:
5	chr19:39950441..39952521-chr19:39955267..39958188,2	MCF-7	breast:
6	chr19:39922266..39923824-chr19:39949808..39952006,2	K562	blood:

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10412931	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs10423537	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10424217	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110627	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1130180	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12609112	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12978920	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978954	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12979605	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12983040	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1529732	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1560730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17626	0.87[CHB][hapmap]
rs1865091	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1932	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060270	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060272	0.89[EUR][1000 genomes]
rs2116932	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288933	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288934	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304221	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353678	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353679	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs251855	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs251856	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs251857	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs251858	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs251859	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs251860	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28528765	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28637729	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28649498	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31727	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs31728	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34918990	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35647910	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4390710	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802026	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803237	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803241	0.90[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803242	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803245	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803246	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803247	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803250	0.85[EUR][1000 genomes]
rs481421	0.86[CHB][hapmap]
rs504017	0.83[ASN][1000 genomes]
rs530411	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs564577	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs566130	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59007555	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508862	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508863	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508864	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508865	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs651601	0.86[CHB][hapmap]
rs686956	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251384	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251652	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255253	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73035416	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73549933	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107647	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8110716	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8111260	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878754	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2060271	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs2060271	RPS16	cis	Lymphoblastoid	GTEx
rs2060271	RPS16	cis	multi-tissue	Pritchard
rs2060271	RPS16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
3	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:39939000-39953400	Strong transcription	Fetal Intestine Small	intestine
5	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
6	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
7	chr19:39940000-39952200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
13	chr19:39941200-39952800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:39941200-39953200	Strong transcription	Dnd41	blood
15	chr19:39941200-39954200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:39941400-39952200	Strong transcription	Fetal Brain Female	brain
17	chr19:39941400-39967400	Strong transcription	Fetal Intestine Large	intestine
18	chr19:39942000-39967400	Strong transcription	Thymus	Thymus
19	chr19:39942000-39967600	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:39942200-39953200	Strong transcription	Brain Angular Gyrus	brain
21	chr19:39942200-39967600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr19:39942200-39967600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:39942200-39967600	Strong transcription	Placenta	Placenta
24	chr19:39942200-39967600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:39942200-39967800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:39942400-39952400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr19:39942400-39953400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:39942600-39953800	Strong transcription	Ovary	ovary
29	chr19:39942600-39967600	Strong transcription	Liver	Liver
30	chr19:39942800-39967400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:39942800-39967800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:39943000-39952200	Strong transcription	GM12878-XiMat	blood
33	chr19:39943000-39952400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:39943000-39967200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr19:39943000-39967800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:39943200-39967800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:39943400-39967400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:39944000-39953600	Strong transcription	Left Ventricle	heart
39	chr19:39944000-39967400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:39945200-39952200	Strong transcription	Rectal Smooth Muscle	rectum
41	chr19:39945400-39952200	Strong transcription	Esophagus	oesophagus
42	chr19:39945800-39955400	Weak transcription	Hela-S3	cervix
43	chr19:39945800-39966200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:39946600-39952200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:39946600-39967600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39946600-39967600	Strong transcription	Primary B cells from cord blood	blood
47	chr19:39946600-39967800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:39946800-39952200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:39946800-39953200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:39946800-39953200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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