Variant report

Variant	rs9288024
Chromosome Location	chr2:179976876-179976877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10172589	0.85[ASN][1000 genomes]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10178559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10186707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10207754	1.00[AMR][1000 genomes]
rs10208882	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10209875	1.00[CHB][hapmap]
rs10221811	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12328593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12329222	0.81[AFR][1000 genomes]
rs12611473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12612427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12613089	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12616452	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12617364	1.00[AMR][1000 genomes]
rs12622434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13382573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383806	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13391187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13395559	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13408774	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13412820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13417112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13422693	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13424092	1.00[CHB][hapmap]
rs13429191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866647	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs28362046	0.85[ASN][1000 genomes]
rs28508327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35041512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7581898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588135	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7601965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7608106	1.00[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
3	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
4	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
7	chr2:179970400-179977000	Weak transcription	Lung	lung
8	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
9	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:179971200-179977600	Strong transcription	Fetal Lung	lung
11	chr2:179971200-179977800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:179971400-179979200	Weak transcription	Ovary	ovary
13	chr2:179971600-179977000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:179971600-179977000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:179971600-179977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:179971600-179979400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:179971800-179978400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:179972200-179982400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:179972400-179977600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:179972400-179979800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:179972400-179982200	Strong transcription	Liver	Liver
26	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:179972600-179977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:179972600-179977600	Strong transcription	Brain Germinal Matrix	brain
31	chr2:179972600-179979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:179972600-179979800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:179972600-179985200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:179972600-179985200	Weak transcription	Fetal Heart	heart
35	chr2:179972600-180001800	Weak transcription	NHEK	skin
36	chr2:179972800-179977600	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:179972800-179979400	Weak transcription	Thymus	Thymus
38	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:179973000-179977000	Weak transcription	NH-A	brain
41	chr2:179973000-179982400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:179973000-179982600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:179973000-179985800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
46	chr2:179973200-179977800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:179973200-179979200	Weak transcription	Hela-S3	cervix
48	chr2:179973200-179979800	Weak transcription	Fetal Intestine Small	intestine
49	chr2:179973200-179980800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:179973200-179982200	Weak transcription	Colonic Mucosa	Colon

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