Variant report

Variant	rs5019497
Chromosome Location	chr1:92265633-92265634
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92262741..92265780-chr1:92267189..92269576,3	K562	blood:
2	chr1:92258357..92261493-chr1:92263209..92266078,3	K562	blood:
3	chr1:92258357..92261637-chr1:92263209..92266078,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1017956	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1017957	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs10493858	0.86[YRI][hapmap]
rs10783036	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10783037	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10783040	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10874940	0.89[CHB][hapmap]
rs10874941	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10874976	0.89[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs10874981	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874996	0.97[YRI][hapmap]
rs10875001	0.96[YRI][hapmap]
rs11165489	0.89[CHB][hapmap]
rs11165496	0.89[ASN][1000 genomes]
rs11165532	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11466573	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192530	0.89[ASN][1000 genomes]
rs12090296	0.89[CHB][hapmap]
rs12756024	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1411276	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs1473486	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1473488	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1473767	0.86[ASN][1000 genomes]
rs2046739	0.82[EUR][1000 genomes]
rs2129975	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2171584	0.85[ASN][1000 genomes]
rs2297142	0.93[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs2391068	0.89[CHB][hapmap]
rs2391069	0.89[CHB][hapmap]
rs2489190	0.89[EUR][1000 genomes]
rs2634031	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2799537	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs4658113	0.88[ASN][1000 genomes]
rs4658268	0.88[ASN][1000 genomes]
rs4658275	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6604054	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6604055	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6604056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669044	0.89[CHB][hapmap]
rs6678564	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs6683840	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6691098	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs7521065	0.82[CHB][hapmap]
rs7530883	0.88[ASN][1000 genomes]
rs7534318	0.89[CHB][hapmap]
rs7536947	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92248200-92268800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:92248600-92268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:92254000-92269400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:92257600-92279400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:92257800-92269600	Weak transcription	A549	lung
6	chr1:92258000-92268400	Weak transcription	Fetal Thymus	thymus
7	chr1:92258200-92269400	Weak transcription	Hela-S3	cervix
8	chr1:92258400-92271400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:92258600-92268600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:92258600-92270000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:92258800-92272400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:92260400-92271200	Strong transcription	HepG2	liver
13	chr1:92260800-92268800	Weak transcription	Small Intestine	intestine
14	chr1:92261800-92268600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:92262200-92268400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:92262200-92269200	Weak transcription	Fetal Kidney	kidney
17	chr1:92262200-92269400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:92262600-92265800	Enhancers	Right Ventricle	heart
19	chr1:92262800-92265800	Enhancers	Left Ventricle	heart
20	chr1:92262800-92277000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:92263000-92265800	Enhancers	Ovary	ovary
22	chr1:92263000-92266200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:92263000-92268000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:92263000-92269200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:92263000-92269600	Weak transcription	Liver	Liver
26	chr1:92263000-92270000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:92263200-92265800	Enhancers	NHDF-Ad	bronchial
28	chr1:92263200-92268600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:92263400-92266000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:92263600-92265800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:92263600-92266400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:92263800-92265800	Enhancers	Colon Smooth Muscle	Colon
33	chr1:92264000-92265800	Enhancers	Pancreas	Pancrea
34	chr1:92264200-92268200	Weak transcription	Esophagus	oesophagus
35	chr1:92264400-92265800	Enhancers	NHLF	lung
36	chr1:92264400-92268400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:92264400-92268800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:92264400-92269000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:92264600-92271800	Weak transcription	Aorta	Aorta
40	chr1:92264800-92265800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:92264800-92268200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:92264800-92269000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:92264800-92269600	Weak transcription	Osteobl	bone
44	chr1:92264800-92284200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:92265000-92265800	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:92265000-92266000	Weak transcription	Spleen	Spleen
47	chr1:92265000-92266800	Weak transcription	Fetal Lung	lung
48	chr1:92265000-92267400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:92265000-92268200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:92265000-92268400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links