Variant report

Variant	rs611928
Chromosome Location	chr6:34279400-34279401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs16885998	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs16889706	0.86[CHD][hapmap]
rs169584	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1811968	0.82[EUR][1000 genomes]
rs2006833	0.84[EUR][1000 genomes]
rs206919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs206920	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs206921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206924	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs206936	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs206942	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237098	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798556	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798562	0.82[CHD][hapmap]
rs3913009	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3913010	0.83[EUR][1000 genomes]
rs410340	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs414739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs458576	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs464553	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711390	0.86[CHD][hapmap]
rs4713770	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4713777	0.86[CHD][hapmap]
rs568502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57622072	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6907486	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6912971	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6924482	0.83[EUR][1000 genomes]
rs6924682	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs6924982	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925243	0.94[ASW][hapmap];0.91[CHD][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap]
rs6930978	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7752035	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7757586	0.83[EUR][1000 genomes]
rs7757900	0.83[EUR][1000 genomes]
rs7765498	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368813	0.83[EUR][1000 genomes]
rs9380433	0.82[EUR][1000 genomes]
rs9394214	0.84[EUR][1000 genomes]
rs9394215	0.82[EUR][1000 genomes]
rs9461981	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9469775	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9469779	0.84[EUR][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	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1794528	chr6:34267024-34308816	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs611928	NUDT3	Cis_1M	lymphoblastoid	RTeQTL
rs611928	RPS10	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:34262000-34282600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:34262000-34282800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:34262000-34283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:34262000-34284600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:34262000-34286600	Weak transcription	Gastric	stomach
8	chr6:34262000-34289000	Weak transcription	Hela-S3	cervix
9	chr6:34262000-34292800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:34262800-34290800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:34263800-34282800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:34263800-34288400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:34264000-34282400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:34264000-34299000	Weak transcription	Dnd41	blood
17	chr6:34264600-34282400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:34264600-34284400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:34267400-34283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:34268600-34283400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:34269400-34282200	Weak transcription	Fetal Thymus	thymus
22	chr6:34269400-34282400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:34269600-34279600	Weak transcription	NH-A	brain
24	chr6:34269600-34280400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:34269600-34280600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:34269600-34286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:34269800-34284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:34270000-34282000	Weak transcription	GM12878-XiMat	blood
29	chr6:34270000-34283600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:34272600-34288200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:34273600-34283000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:34274000-34283600	Weak transcription	Fetal Kidney	kidney
33	chr6:34274200-34285000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:34274200-34285000	Weak transcription	HSMMtube	muscle
35	chr6:34274400-34282600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:34274400-34282600	Weak transcription	Brain Anterior Caudate	brain
37	chr6:34274400-34306400	Weak transcription	Brain Germinal Matrix	brain
38	chr6:34274400-34309000	Weak transcription	NHDF-Ad	bronchial
39	chr6:34274600-34281000	Weak transcription	Primary B cells from cord blood	blood
40	chr6:34274600-34283000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:34274800-34285200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:34275000-34284200	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:34275000-34285400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:34275200-34285800	Weak transcription	Fetal Stomach	stomach
45	chr6:34275200-34298000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:34275400-34284400	Weak transcription	Right Ventricle	heart
47	chr6:34275400-34285200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:34275400-34286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:34275400-34289400	Weak transcription	HUVEC	blood vessel
50	chr6:34275600-34283600	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links