Variant report

Variant	rs4750495
Chromosome Location	chr10:6501445-6501446
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10906569	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11258536	0.83[GIH][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap]
rs11258759	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11258762	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11258959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11258960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11816284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12146312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453	1.00[ASW][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4364968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[ASN][1000 genomes]
rs4750434	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4750439	0.92[CHD][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs4750457	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4750461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4750470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4750491	0.90[MEX][hapmap]
rs586457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs594841	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6602699	0.95[ASN][1000 genomes]
rs670804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677986	0.83[CEU][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs681803	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs688391	0.81[MEX][hapmap]
rs7076533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7099451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918373	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7920048	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs943456	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944712	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs944713	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs944715	0.83[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4750495	CALML5	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6477400-6503600	Weak transcription	Gastric	stomach
2	chr10:6488200-6502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:6488400-6506800	Weak transcription	K562	blood
4	chr10:6493400-6516200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:6496000-6502800	Strong transcription	Dnd41	blood
6	chr10:6496000-6508200	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:6496200-6501600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr10:6496200-6501600	Strong transcription	Fetal Muscle Leg	muscle
9	chr10:6496200-6502000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:6496200-6502800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr10:6496200-6506200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:6496200-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:6496200-6509000	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:6496200-6511600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:6496200-6513000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:6496200-6514000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:6496200-6514200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:6496200-6514600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:6496400-6502000	Strong transcription	Brain Hippocampus Middle	brain
20	chr10:6496600-6506400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr10:6496800-6503000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr10:6497600-6501600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:6497600-6513200	Strong transcription	Primary T cells from cord blood	blood
25	chr10:6497800-6502200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr10:6497800-6502800	Weak transcription	Fetal Kidney	kidney
27	chr10:6498400-6501600	Weak transcription	Psoas Muscle	Psoas
28	chr10:6498400-6537000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:6498600-6506000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr10:6498600-6508800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:6498600-6510000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:6498600-6512000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:6498600-6518800	Weak transcription	Fetal Stomach	stomach
34	chr10:6499000-6501800	Genic enhancers	Fetal Thymus	thymus
35	chr10:6499000-6503800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:6499000-6504200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:6499000-6507600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:6499000-6527800	Weak transcription	Pancreas	Pancrea
39	chr10:6499200-6503000	Weak transcription	Brain Angular Gyrus	brain
40	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
41	chr10:6499400-6502600	Genic enhancers	Thymus	Thymus
42	chr10:6499600-6501800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:6499600-6502800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:6499800-6501800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr10:6500200-6501600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:6500200-6501800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:6500200-6501800	ZNF genes & repeats	Aorta	Aorta
48	chr10:6500200-6502000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr10:6500200-6502000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr10:6500200-6504400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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