Variant report

Variant	rs10741127
Chromosome Location	chr10:18957647-18957648
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1055116	0.84[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10734063	0.81[EUR][1000 genomes]
rs10741091	0.88[CEU][hapmap]
rs10741115	0.92[CEU][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs10741129	0.90[EUR][1000 genomes]
rs10741132	0.87[EUR][1000 genomes]
rs10764582	0.83[CEU][hapmap];0.87[YRI][hapmap]
rs10764601	0.84[CEU][hapmap];0.84[YRI][hapmap]
rs10764640	0.86[EUR][1000 genomes]
rs10764691	0.89[EUR][1000 genomes]
rs10828851	0.84[CEU][hapmap];0.95[TSI][hapmap]
rs10828870	0.84[CEU][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs10828871	0.81[CEU][hapmap]
rs10828896	0.84[CEU][hapmap];0.88[YRI][hapmap]
rs10828975	0.88[CEU][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs10829022	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs10829037	0.84[EUR][1000 genomes]
rs10829039	0.84[EUR][1000 genomes]
rs10829058	0.92[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs10829060	0.85[EUR][1000 genomes]
rs10829070	0.88[CEU][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs10829148	0.86[EUR][1000 genomes]
rs10829151	0.92[CEU][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs10829213	0.89[EUR][1000 genomes]
rs11015196	0.84[EUR][1000 genomes]
rs11015312	0.92[CEU][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs11015421	0.91[EUR][1000 genomes]
rs12219183	0.89[EUR][1000 genomes]
rs12359758	0.91[EUR][1000 genomes]
rs12768464	0.85[JPT][hapmap]
rs2272274	0.83[CEU][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap]
rs3740102	0.92[CEU][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs3817494	0.93[TSI][hapmap];0.88[YRI][hapmap]
rs4748483	0.89[GIH][hapmap];0.91[TSI][hapmap]
rs4748488	0.88[CEU][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs4748509	0.87[EUR][1000 genomes]
rs57066269	0.89[EUR][1000 genomes]
rs6482533	0.92[CEU][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs6482597	0.88[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7081690	0.86[EUR][1000 genomes]
rs7081977	0.90[EUR][1000 genomes]
rs7087030	0.89[EUR][1000 genomes]
rs7088091	0.84[CEU][hapmap];0.98[TSI][hapmap]
rs7099260	0.92[CEU][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs7100880	0.93[TSI][hapmap];0.84[YRI][hapmap]
rs7895784	0.84[TSI][hapmap];0.84[YRI][hapmap]
rs7898781	0.90[EUR][1000 genomes]
rs7899017	0.91[EUR][1000 genomes]
rs7909570	0.88[EUR][1000 genomes]
rs7909845	0.89[EUR][1000 genomes]
rs7917584	0.82[CEU][hapmap]
rs7922550	0.84[CEU][hapmap]
rs7922829	0.84[CEU][hapmap];0.80[YRI][hapmap]

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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10741127	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs10741127	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10741127	ARL5B	cis	Liver	GTEx
rs10741127	RP11-499P20.2	cis	Whole Blood	GTEx
rs10741127	ARL5B	cis	multi-tissue	Pritchard
rs10741127	RP11-499P20.2	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18950800-18962400	Weak transcription	Fetal Kidney	kidney
4	chr10:18951000-18961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:18951000-18962400	Weak transcription	Fetal Lung	lung
6	chr10:18951000-18965800	Weak transcription	Colonic Mucosa	Colon
7	chr10:18951000-18966600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:18951000-18967400	Weak transcription	Esophagus	oesophagus
9	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
10	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:18951200-18964400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:18951400-18957800	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:18951400-18962400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:18951400-18962800	Weak transcription	Fetal Brain Male	brain
15	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
16	chr10:18954000-18959400	Weak transcription	Ovary	ovary
17	chr10:18954000-18960200	Weak transcription	Lung	lung
18	chr10:18954000-18966600	Strong transcription	Dnd41	blood
19	chr10:18954400-18962200	Weak transcription	Psoas Muscle	Psoas
20	chr10:18954400-18964400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:18954400-18967200	Weak transcription	Gastric	stomach
22	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
23	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:18954600-18959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:18954800-18959800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:18954800-18962800	Weak transcription	K562	blood
27	chr10:18954800-18964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:18955200-18958400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:18955200-18959400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:18955200-18967600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:18955400-18959400	Weak transcription	Fetal Brain Female	brain
33	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
34	chr10:18955600-18966600	Strong transcription	Primary B cells from cord blood	blood
35	chr10:18955600-18966600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:18955600-18968000	Weak transcription	Brain Substantia Nigra	brain
37	chr10:18955800-18960800	Strong transcription	Fetal Thymus	thymus
38	chr10:18955800-18961000	Strong transcription	Fetal Intestine Large	intestine
39	chr10:18955800-18966200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:18955800-18966600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:18956000-18957800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr10:18956000-18957800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr10:18956000-18958600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr10:18956000-18966200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr10:18956000-18966200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:18956000-18966600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:18956000-18966800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:18956200-18958200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links