Variant report

Variant	rs10509688
Chromosome Location	chr10:97385242-97385243
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	chr10:97384935..97386952-chr10:97417670..97420047,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10882658	0.83[AFR][1000 genomes]
rs11188409	0.95[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs11188426	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11188427	0.89[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs12414244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12414904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270505	0.82[CHD][hapmap]
rs12768006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12769303	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12783226	0.84[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1933164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485642	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861150	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs3176894	0.84[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs34297443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35087577	0.81[AMR][1000 genomes]
rs4481960	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs476392	0.86[ASN][1000 genomes]
rs483920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4918949	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918959	0.83[AFR][1000 genomes]
rs561156	0.86[ASN][1000 genomes]
rs568401	0.86[ASN][1000 genomes]
rs7090916	0.83[AFR][1000 genomes]
rs7096610	0.82[JPT][hapmap]
rs72813744	0.81[AMR][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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10509688	NOC3L	cis	parietal	SCAN
rs10509688	GPR120	cis	parietal	SCAN
rs10509688	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs10509688	ENTPD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
2	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:97367400-97388600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:97367600-97388400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:97368400-97393000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:97373800-97386600	Weak transcription	Fetal Brain Male	brain
13	chr10:97374000-97386400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:97374400-97386600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr10:97375400-97387000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:97376200-97400600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:97376400-97411400	Weak transcription	Psoas Muscle	Psoas
18	chr10:97376400-97415200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:97376600-97385800	Weak transcription	Fetal Kidney	kidney
20	chr10:97376600-97415000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:97378200-97386400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:97378200-97387200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:97378200-97391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr10:97378600-97385800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:97378600-97386400	Weak transcription	Spleen	Spleen
26	chr10:97378600-97414200	Weak transcription	Fetal Heart	heart
27	chr10:97378800-97387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr10:97378800-97388000	Weak transcription	K562	blood
29	chr10:97379800-97403200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:97380200-97386600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr10:97380200-97399200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:97380200-97403200	Strong transcription	Fetal Muscle Leg	muscle
33	chr10:97380200-97403400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:97380200-97408800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr10:97380400-97386600	Weak transcription	Fetal Lung	lung
36	chr10:97380600-97385800	Strong transcription	Fetal Intestine Large	intestine
37	chr10:97380600-97387400	Strong transcription	Fetal Stomach	stomach
38	chr10:97380600-97403000	Strong transcription	NH-A	brain
39	chr10:97380600-97403200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:97380600-97403200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:97380600-97408000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:97380800-97388800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:97380800-97409000	Strong transcription	Osteobl	bone
44	chr10:97381000-97385800	Weak transcription	Esophagus	oesophagus
45	chr10:97381000-97391600	Weak transcription	Brain Angular Gyrus	brain
46	chr10:97381200-97385800	Weak transcription	Lung	lung
47	chr10:97381200-97385800	Weak transcription	Stomach Mucosa	stomach
48	chr10:97381200-97403400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr10:97381400-97385800	Strong transcription	Fetal Intestine Small	intestine
50	chr10:97381400-97393000	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links