Variant report

Variant	rs333165
Chromosome Location	chr1:61714304-61714305
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	chr1:61711526..61714321-chr1:61724717..61727346,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11207719	0.82[EUR][1000 genomes]
rs12082781	1.00[YRI][hapmap]
rs162878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121858	0.82[CHB][hapmap];0.87[MKK][hapmap];0.83[ASN][1000 genomes]
rs186742	0.82[MEX][hapmap]
rs1977653	0.83[EUR][1000 genomes]
rs2275208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333136	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333138	0.82[AMR][1000 genomes]
rs333140	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333142	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333143	0.92[JPT][hapmap]
rs333144	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333145	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333146	0.92[JPT][hapmap];0.89[MKK][hapmap]
rs333147	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs333148	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs333150	0.89[CEU][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes]
rs333160	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333162	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs333164	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333166	1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334690	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684051	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs72664877	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664888	0.85[EUR][1000 genomes]
rs72664890	0.85[EUR][1000 genomes]
rs72664891	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61680000-61720200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:61705400-61715200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:61707400-61718800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:61707400-61718800	Weak transcription	Gastric	stomach
5	chr1:61707600-61719000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:61707800-61718600	Weak transcription	Stomach Mucosa	stomach
7	chr1:61708000-61718800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:61708000-61720400	Weak transcription	Colonic Mucosa	Colon
9	chr1:61709600-61719000	Weak transcription	Lung	lung
10	chr1:61710200-61715600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:61710200-61715600	Weak transcription	Fetal Heart	heart
12	chr1:61710200-61716600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:61710200-61718800	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:61710200-61718800	Weak transcription	Small Intestine	intestine
15	chr1:61710200-61720400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:61710400-61718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:61710400-61718800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:61710400-61718800	Weak transcription	Fetal Stomach	stomach
19	chr1:61710600-61716000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:61712800-61714600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:61713000-61714400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:61713000-61714800	Enhancers	Fetal Lung	lung
23	chr1:61713000-61715000	Enhancers	Brain Substantia Nigra	brain
24	chr1:61713200-61714400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:61713200-61714400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:61713200-61714400	Enhancers	Brain Hippocampus Middle	brain
27	chr1:61713200-61714600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:61713200-61714600	Enhancers	Liver	Liver
29	chr1:61713200-61716000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:61713200-61718800	Weak transcription	Fetal Brain Male	brain
31	chr1:61713400-61715600	Weak transcription	Fetal Brain Female	brain
32	chr1:61713400-61716200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr1:61713400-61717000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:61713400-61717000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:61713400-61718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:61713400-61718600	Weak transcription	Pancreas	Pancrea
37	chr1:61713400-61718600	Weak transcription	Right Atrium	heart
38	chr1:61713400-61718600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:61713400-61718600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:61713400-61718800	Weak transcription	Left Ventricle	heart
41	chr1:61713600-61714600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:61713600-61714600	Enhancers	Colon Smooth Muscle	Colon
43	chr1:61713600-61714800	Enhancers	Brain Anterior Caudate	brain
44	chr1:61713600-61716000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr1:61713800-61714400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:61713800-61714400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:61713800-61714400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:61713800-61714600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:61713800-61714600	Enhancers	Adipose Nuclei	Adipose
50	chr1:61713800-61715200	Weak transcription	Ovary	ovary

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