Variant report

Variant	rs16852004
Chromosome Location	chr3:141646962-141646963
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	chr3:141645508..141649980-chr3:141650119..141655905,6	K562	blood:
2	chr3:141646387..141648492-chr3:141652894..141655843,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10804680	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717068	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3765155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3828400	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56348155	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6774412	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6799078	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848990	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9869659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16852004	CHST2	cis	cerebellum	SCAN
rs16852004	PCOLCE2	cis	cerebellum	SCAN
rs16852004	NMNAT3	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
3	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
6	chr3:141624600-141649200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:141625600-141647200	Weak transcription	Liver	Liver
8	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
10	chr3:141627600-141649200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:141627800-141652600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
16	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
18	chr3:141630000-141647000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:141630600-141647400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:141630600-141647400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:141631200-141647600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:141632000-141647400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:141632000-141648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:141632200-141647800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:141632200-141648000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:141632400-141654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:141633000-141659000	Weak transcription	NHLF	lung
28	chr3:141633600-141648000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:141634200-141648600	Weak transcription	Aorta	Aorta
30	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:141634400-141648600	Weak transcription	Fetal Kidney	kidney
32	chr3:141634400-141656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:141635400-141648200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:141635400-141648600	Strong transcription	Fetal Intestine Large	intestine
35	chr3:141635800-141652400	Weak transcription	HSMM	muscle
36	chr3:141635800-141652600	Strong transcription	Thymus	Thymus
37	chr3:141636200-141647800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:141636200-141648000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:141637400-141658800	Weak transcription	Brain Germinal Matrix	brain
40	chr3:141638200-141648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:141638600-141648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:141640200-141648200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:141640200-141650200	Weak transcription	GM12878-XiMat	blood
44	chr3:141640600-141656400	Weak transcription	Fetal Brain Male	brain
45	chr3:141640600-141658800	Weak transcription	Fetal Heart	heart
46	chr3:141640800-141659200	Weak transcription	Colonic Mucosa	Colon
47	chr3:141640800-141659200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:141641000-141652800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:141641200-141648200	Weak transcription	HepG2	liver
50	chr3:141641200-141648800	Strong transcription	Fetal Stomach	stomach

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