Variant report

Variant	rs17628946
Chromosome Location	chr6:34260257-34260258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34251031..34253241-chr6:34259138..34261085,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10484267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484268	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1057691	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1060308	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10648	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1127084	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13466	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883137	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883896	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17628798	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17629180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206922	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3798558	1.00[YRI][hapmap]
rs41269032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269034	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269036	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55684754	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55694290	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763242	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55779010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55798596	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55833185	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55864834	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039915	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56107559	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56188036	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56274913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323997	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911272	0.88[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7738665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741127	0.80[AMR][1000 genomes]
rs7760373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770443	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs875274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368811	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17628946	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
3	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:34245000-34262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:34245000-34263400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:34245200-34260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:34245400-34260800	Weak transcription	Aorta	Aorta
8	chr6:34245600-34261600	Weak transcription	Gastric	stomach
9	chr6:34246000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:34246600-34264000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:34246600-34264000	Strong transcription	Dnd41	blood
12	chr6:34247800-34260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:34250600-34261000	Weak transcription	Colonic Mucosa	Colon
14	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:34253000-34260800	Weak transcription	A549	lung
16	chr6:34253600-34271200	Weak transcription	Stomach Mucosa	stomach
17	chr6:34255000-34263800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:34255200-34263800	Strong transcription	Fetal Stomach	stomach
19	chr6:34255600-34260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:34256600-34260600	Weak transcription	Thymus	Thymus
21	chr6:34256600-34260800	Weak transcription	Fetal Brain Female	brain
22	chr6:34256600-34264400	Weak transcription	Right Atrium	heart
23	chr6:34256800-34260600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:34256800-34260800	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:34256800-34261000	Weak transcription	Small Intestine	intestine
26	chr6:34257000-34264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:34257200-34260400	Weak transcription	Primary T cells from cord blood	blood
28	chr6:34257200-34260800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:34257800-34260400	Weak transcription	Psoas Muscle	Psoas
30	chr6:34258000-34261000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:34258000-34262000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:34258200-34262000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:34258200-34263600	Strong transcription	Fetal Muscle Leg	muscle
34	chr6:34258200-34263800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:34258400-34262200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:34258600-34263200	Strong transcription	Fetal Intestine Small	intestine
37	chr6:34258800-34262000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:34258800-34264600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:34259200-34262000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:34259200-34262000	Strong transcription	Fetal Thymus	thymus
41	chr6:34259200-34262200	Strong transcription	Adipose Nuclei	Adipose
42	chr6:34259200-34262800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:34259200-34263000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:34259200-34263000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:34259200-34263000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:34259200-34263600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr6:34259200-34263600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:34259200-34264000	Strong transcription	HepG2	liver
49	chr6:34259400-34260400	Strong transcription	Left Ventricle	heart
50	chr6:34259400-34261400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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