Variant report

Variant	rs2008999
Chromosome Location	chr2:179971332-179971333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179966762..179969783-chr2:179969877..179973075,3	K562	blood:
2	chr2:179967469..179969783-chr2:179970648..179973075,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10170520	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10174774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs10186198	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10192426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205390	0.94[JPT][hapmap];0.88[YRI][hapmap]
rs10205999	0.83[AFR][1000 genomes]
rs10439299	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10930858	0.82[AFR][1000 genomes]
rs1158872	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11884516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11894870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11898291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12997314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs13026497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs13383965	0.82[EUR][1000 genomes]
rs13391602	0.84[EUR][1000 genomes]
rs13418701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1374378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1374379	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446674	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1979053	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4585064	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433757	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433761	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433764	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6734121	0.83[AFR][1000 genomes]
rs6736098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6742744	0.82[YRI][hapmap]
rs6743405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757681	0.90[YRI][hapmap]
rs7579536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs7608882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs873023	0.88[YRI][hapmap]
rs9288022	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008999	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179961600-179972400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:179961600-179972800	Weak transcription	Spleen	Spleen
3	chr2:179961600-179974000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:179961800-179972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:179962000-179972600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:179962000-179972800	Weak transcription	Fetal Thymus	thymus
7	chr2:179962400-179972600	Weak transcription	Left Ventricle	heart
8	chr2:179962800-179972400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:179965200-179971400	Weak transcription	Brain Germinal Matrix	brain
10	chr2:179966200-179973000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:179966400-179972400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:179966400-179972600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:179966400-179975600	Weak transcription	Aorta	Aorta
14	chr2:179966600-179971600	Weak transcription	Fetal Brain Female	brain
15	chr2:179966600-179972400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:179967000-179972200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:179967200-179976800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:179967400-179971800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
21	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
22	chr2:179969000-179972400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:179969200-179972000	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:179969200-179972800	Enhancers	Colon Smooth Muscle	Colon
25	chr2:179969200-179973000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:179969400-179972400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:179969600-179973000	Enhancers	HMEC	breast
29	chr2:179969800-179972600	Enhancers	Brain Substantia Nigra	brain
30	chr2:179970000-179972800	Weak transcription	Placenta	Placenta
31	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:179970200-179972000	Enhancers	Brain Anterior Caudate	brain
33	chr2:179970200-179972600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
35	chr2:179970400-179971400	Weak transcription	NHLF	lung
36	chr2:179970400-179972800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:179970400-179977000	Weak transcription	Lung	lung
38	chr2:179970600-179972600	Enhancers	NHEK	skin
39	chr2:179970600-179973800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:179970800-179971800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:179970800-179972000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:179970800-179972200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:179970800-179972400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:179970800-179972400	Weak transcription	Liver	Liver
45	chr2:179970800-179972400	Enhancers	Osteobl	bone
46	chr2:179970800-179973000	Enhancers	HSMMtube	muscle
47	chr2:179970800-179973200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:179970800-179973200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr2:179970800-179973200	Enhancers	Fetal Intestine Small	intestine
50	chr2:179970800-179973200	Enhancers	Pancreatic Islets	Pancreatic Islet

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