Variant report

Variant	rs1182098
Chromosome Location	chr1:86820267-86820268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10493790	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11161810	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161812	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161814	0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161816	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161817	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161831	0.83[CEU][hapmap]
rs1158833	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1182099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1182101	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119411	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123660	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12125965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130284	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12145243	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12146009	0.81[CEU][hapmap]
rs12403033	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12406320	0.86[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1323036	0.89[AMR][1000 genomes]
rs1413431	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1413432	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17409213	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17409304	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17449526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1931360	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1931361	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1931362	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs272486	0.88[AMR][1000 genomes]
rs272488	0.94[ASN][1000 genomes]
rs272489	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272490	0.97[ASN][1000 genomes]
rs272493	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272495	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272496	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272497	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272499	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272500	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs272501	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272505	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272506	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs272509	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272512	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272514	1.00[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs272515	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272518	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35489949	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3737673	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3765983	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs423991	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5026277	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56104000	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56408800	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57210989	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61124915	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6688340	0.89[AMR][1000 genomes]
rs72720129	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs969396	0.81[AMR][1000 genomes]
rs977919	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1792405	chr1:86814270-86825639	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86806400-86823600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:86813800-86836400	Weak transcription	Lung	lung
4	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
5	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
6	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:86816200-86824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:86816200-86826200	Weak transcription	A549	lung
9	chr1:86816400-86820400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:86817200-86820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:86817200-86820400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
13	chr1:86817400-86820600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:86817400-86820800	Strong transcription	Dnd41	blood
15	chr1:86817400-86821000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:86817400-86824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:86817400-86824400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:86817400-86826000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:86817400-86826000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:86817400-86826200	Strong transcription	HUVEC	blood vessel
21	chr1:86817600-86820400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:86817600-86820400	Strong transcription	Liver	Liver
23	chr1:86817600-86820400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:86817600-86820600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:86817600-86821400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:86817600-86825200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:86817600-86825400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:86817600-86826000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:86817600-86826200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:86817800-86820400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:86817800-86820400	Strong transcription	Adipose Nuclei	Adipose
33	chr1:86817800-86820600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:86817800-86828000	Weak transcription	Fetal Stomach	stomach
35	chr1:86817800-86828000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:86817800-86835400	Weak transcription	Esophagus	oesophagus
37	chr1:86817800-86840000	Weak transcription	GM12878-XiMat	blood
38	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:86818000-86820400	Strong transcription	HSMM	muscle
40	chr1:86818000-86822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:86818000-86822400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
43	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
44	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:86818200-86820400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:86818200-86820600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:86818200-86841000	Weak transcription	Fetal Kidney	kidney
48	chr1:86818400-86820400	Strong transcription	NH-A	brain
49	chr1:86818400-86821000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:86818400-86821000	Weak transcription	Psoas Muscle	Psoas

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