Variant report

Variant	rs9814578
Chromosome Location	chr3:45863267-45863268
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45861974..45863504-chr3:45865179..45867037,2	K562	blood:
2	chr3:45862583..45864732-chr3:45872437..45875111,2	K562	blood:
3	chr3:45734225..45736737-chr3:45860844..45863689,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1058961	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs11130076	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13065964	0.91[CHB][hapmap]
rs1386930	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1488369	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1860264	0.81[JPT][hapmap]
rs2064061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683146	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441930	0.81[JPT][hapmap]
rs7613548	0.81[JPT][hapmap]
rs7625839	0.86[CHB][hapmap]
rs9868455	0.81[JPT][hapmap]
rs9871972	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9814578	CCR1	cis	cerebellum	SCAN
rs9814578	CDC25A	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:45848000-45864400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:45849400-45864800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:45850200-45866200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:45850200-45867800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:45850600-45868200	Weak transcription	Spleen	Spleen
9	chr3:45857800-45863600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:45857800-45871600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:45858000-45882600	Weak transcription	A549	lung
12	chr3:45858200-45863600	Weak transcription	Lung	lung
13	chr3:45858400-45866000	Weak transcription	Fetal Brain Male	brain
14	chr3:45858400-45868400	Weak transcription	Fetal Kidney	kidney
15	chr3:45858400-45881200	Strong transcription	Dnd41	blood
16	chr3:45859400-45865000	Strong transcription	Brain Germinal Matrix	brain
17	chr3:45859400-45866000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:45859400-45868400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:45859600-45866000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:45859800-45871400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:45860000-45863600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:45860000-45863600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:45860000-45864800	Strong transcription	Fetal Stomach	stomach
24	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:45860200-45867600	Weak transcription	GM12878-XiMat	blood
27	chr3:45860400-45863400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:45860400-45863800	Weak transcription	Ovary	ovary
29	chr3:45860400-45864400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:45860400-45864800	Strong transcription	Thymus	Thymus
31	chr3:45860400-45867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:45860400-45868000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:45860400-45868200	Strong transcription	Fetal Thymus	thymus
34	chr3:45860400-45868200	Weak transcription	Pancreas	Pancrea
35	chr3:45860400-45871600	Weak transcription	Esophagus	oesophagus
36	chr3:45860400-45871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:45860400-45871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:45860400-45875800	Weak transcription	Placenta	Placenta
39	chr3:45860400-45877400	Strong transcription	Liver	Liver
40	chr3:45860600-45864000	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:45860600-45865400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:45860600-45865800	Weak transcription	Osteobl	bone
43	chr3:45860600-45866000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:45860600-45874400	Weak transcription	HUVEC	blood vessel
45	chr3:45860800-45866000	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:45860800-45867200	Strong transcription	Primary T cells from cord blood	blood
47	chr3:45860800-45868400	Weak transcription	Gastric	stomach
48	chr3:45860800-45875200	Weak transcription	Aorta	Aorta
49	chr3:45861000-45882400	Weak transcription	Small Intestine	intestine
50	chr3:45861000-45882400	Weak transcription	NHDF-Ad	bronchial

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