Variant report

Variant	rs10084475
Chromosome Location	chr2:180004813-180004814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179990644..179992721-chr2:180003873..180005520,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10084229	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170430	0.87[EUR][1000 genomes]
rs10173710	0.93[AFR][1000 genomes]
rs10196577	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10205477	0.85[ASN][1000 genomes]
rs10208593	0.85[AFR][1000 genomes]
rs10930855	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930856	0.88[ASN][1000 genomes]
rs12615736	0.91[AFR][1000 genomes]
rs12693175	1.00[ASN][1000 genomes]
rs13021442	0.87[ASN][1000 genomes]
rs13022867	0.85[ASN][1000 genomes]
rs13029576	0.88[ASN][1000 genomes]
rs13396334	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403231	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13404037	0.88[ASN][1000 genomes]
rs13420572	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363260	1.00[ASN][1000 genomes]
rs17363267	1.00[ASN][1000 genomes]
rs17454311	0.94[AFR][1000 genomes]
rs1900338	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2289993	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289994	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28763731	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34728717	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55750558	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56109193	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181927	0.88[ASN][1000 genomes]
rs67028844	0.88[ASN][1000 genomes]
rs67312569	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10084475	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
6	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
7	chr2:179973400-180012600	Weak transcription	NHLF	lung
8	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
11	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
12	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:179980000-180038800	Weak transcription	HMEC	breast
14	chr2:179980000-180056800	Weak transcription	HSMM	muscle
15	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:179981400-180005000	Weak transcription	Ovary	ovary
18	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:179981800-180005400	Weak transcription	Osteobl	bone
21	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:179984800-180005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:179985600-180005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:179985800-180005800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:179985800-180010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:179986200-180006000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:179990800-180005000	Weak transcription	Thymus	Thymus
30	chr2:179991600-180005000	Weak transcription	Brain Substantia Nigra	brain
31	chr2:179991600-180005600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:179991600-180007200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
34	chr2:179991800-180006000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:179992200-180014600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:179992400-180005600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:179994800-180005600	Weak transcription	Fetal Heart	heart
38	chr2:179995800-180016200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:179996200-180047600	Weak transcription	NH-A	brain
40	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
41	chr2:179999800-180005200	Weak transcription	Primary T cells from cord blood	blood
42	chr2:179999800-180009600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:180000600-180016200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:180000600-180016200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:180001200-180005400	Weak transcription	NHDF-Ad	bronchial
46	chr2:180001200-180016200	Strong transcription	HepG2	liver
47	chr2:180001800-180009000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:180002000-180005000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:180002000-180005000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:180002000-180011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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