Variant report

Variant	rs6661828
Chromosome Location	chr1:175909912-175909913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10436864	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10494496	0.82[CHB][hapmap]
rs10737315	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737316	1.00[CHB][hapmap]
rs10753111	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10798428	0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs10798431	1.00[CHB][hapmap]
rs10798432	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1155229	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11576471	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12029090	0.85[YRI][hapmap]
rs12038027	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1357337	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1522637	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16849522	0.82[CHB][hapmap]
rs1831447	0.82[CHB][hapmap]
rs2039231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap]
rs2481627	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs2481641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2481647	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2481651	0.85[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap]
rs2481657	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502822	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502824	1.00[CHB][hapmap]
rs2502826	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502832	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2502834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs2502835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap]
rs2502836	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2502841	1.00[CHB][hapmap]
rs2502842	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs2861629	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4129061	0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap]
rs4307526	0.90[ASN][1000 genomes]
rs4314844	0.85[ASN][1000 genomes]
rs4543747	1.00[CHB][hapmap]
rs4652143	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4652148	0.82[CHB][hapmap]
rs6425367	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6687043	0.94[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704509	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7517351	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7522442	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7524972	0.95[ASN][1000 genomes]
rs7536464	1.00[CHB][hapmap]
rs7537435	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7537480	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539247	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];0.95[ASN][1000 genomes]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7545639	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7546538	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7552181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7553184	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];0.95[ASN][1000 genomes]
rs9783047	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175874400-175945600	Weak transcription	A549	lung
2	chr1:175880000-175937800	Weak transcription	HSMMtube	muscle
3	chr1:175881000-175924200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:175882600-175910200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:175886400-175929400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:175887800-175929800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:175889200-175937800	Weak transcription	Osteobl	bone
8	chr1:175892400-175940600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:175893200-175943000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:175897600-175911000	Weak transcription	Thymus	Thymus
12	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
15	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
16	chr1:175901600-175940600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:175901800-175925800	Weak transcription	HUVEC	blood vessel
18	chr1:175902400-175914800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:175902400-175917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:175902800-175931800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:175903200-175924200	Weak transcription	Gastric	stomach
22	chr1:175903400-175951400	Weak transcription	K562	blood
23	chr1:175903600-175940800	Weak transcription	HMEC	breast
24	chr1:175903800-175915800	Weak transcription	GM12878-XiMat	blood
25	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
26	chr1:175904400-175911800	Strong transcription	Primary T cells from cord blood	blood
27	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
28	chr1:175904800-175911800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:175905000-175911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:175905000-175911200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:175905000-175946800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:175905200-175911800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:175905200-175916000	Weak transcription	NHDF-Ad	bronchial
34	chr1:175905400-175918800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:175905600-175910200	Weak transcription	Fetal Thymus	thymus
36	chr1:175905600-175911200	Weak transcription	Aorta	Aorta
37	chr1:175905600-175918800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:175906000-175911400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:175906000-175914600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:175906000-175915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:175906000-175915600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:175906000-175918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:175906000-175930000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:175906200-175914800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:175906200-175917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:175906200-175917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:175906200-175919000	Weak transcription	Fetal Brain Male	brain
48	chr1:175906400-175914800	Weak transcription	HSMM	muscle
49	chr1:175906400-175920800	Weak transcription	HepG2	liver
50	chr1:175906400-175940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links