Variant report

Variant	rs162878
Chromosome Location	chr1:61704601-61704602
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	chr1:61701203..61703807-chr1:61704252..61706919,4	K562	blood:
2	chr1:61703917..61705509-chr1:61705785..61707297,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12082781	1.00[YRI][hapmap]
rs167987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121858	0.82[CHB][hapmap];0.87[MKK][hapmap];0.83[ASN][1000 genomes]
rs186742	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs2275208	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333136	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs333138	0.87[AMR][1000 genomes]
rs333140	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs333141	0.81[EUR][1000 genomes]
rs333142	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs333143	0.92[JPT][hapmap]
rs333144	0.87[AMR][1000 genomes]
rs333145	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap];0.87[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]
rs333148	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs333150	0.89[CEU][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes]
rs333160	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs333164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333165	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]
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];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]
rs334690	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]
rs4244151	1.00[CEU][hapmap];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]
rs6684051	0.86[CEU][hapmap]
rs72664877	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1849929	chr1:61684084-61714142	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61680000-61720200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:61682000-61706800	Weak transcription	Gastric	stomach
3	chr1:61692800-61706800	Weak transcription	Fetal Lung	lung
4	chr1:61692800-61707000	Weak transcription	Fetal Stomach	stomach
5	chr1:61692800-61707200	Weak transcription	Pancreas	Pancrea
6	chr1:61693000-61706800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:61693000-61706800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:61694000-61706800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:61694200-61706800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:61694200-61707000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:61696600-61706800	Weak transcription	Right Ventricle	heart
12	chr1:61696600-61707200	Weak transcription	Left Ventricle	heart
13	chr1:61696800-61707000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:61696800-61707200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:61696800-61707200	Weak transcription	Small Intestine	intestine
16	chr1:61699400-61706800	Weak transcription	HepG2	liver
17	chr1:61700800-61707400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:61701600-61705000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:61701600-61706200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:61701600-61706200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:61701600-61707200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:61702400-61706400	Weak transcription	Fetal Heart	heart
23	chr1:61703400-61705400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:61703600-61706800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:61703600-61713600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:61703800-61706800	Weak transcription	A549	lung
27	chr1:61704000-61704800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:61704200-61705000	Enhancers	Fetal Brain Female	brain
29	chr1:61704200-61705600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:61704200-61706800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:61704200-61706800	Weak transcription	NHEK	skin
32	chr1:61704200-61707000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:61704200-61707000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:61704200-61707200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:61704200-61707200	Weak transcription	HMEC	breast
36	chr1:61704400-61705600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:61704400-61706800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:61704400-61706800	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:61704400-61706800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:61704400-61706800	Weak transcription	Brain Substantia Nigra	brain
41	chr1:61704400-61706800	Weak transcription	Fetal Brain Male	brain
42	chr1:61704400-61706800	Weak transcription	Right Atrium	heart
43	chr1:61704600-61706600	Weak transcription	Liver	Liver
44	chr1:61704600-61706800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:61704600-61706800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:61704600-61706800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:61704600-61707200	Weak transcription	K562	blood
48	chr1:61704600-61707800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:61704600-61713400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:61704600-61713600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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