Variant report

Variant	rs7089687
Chromosome Location	chr10:112647761-112647762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10082499	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10787286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787291	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10787293	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10787299	0.84[EUR][1000 genomes]
rs10885059	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885060	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885061	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10885064	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10885071	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10885076	0.80[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs11195361	0.84[ASN][1000 genomes]
rs11195366	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195381	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11195387	0.80[CEU][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11195390	0.80[CEU][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11195391	1.00[JPT][hapmap]
rs11195398	0.80[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12240685	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242177	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12242928	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12246561	0.87[ASW][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs12249031	0.81[AFR][1000 genomes]
rs12258559	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12261765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12776359	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12776861	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12783690	1.00[JPT][hapmap]
rs2146544	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs34401279	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34893229	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35394459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35793075	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750619	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3763692	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917589	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6585026	0.80[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs7070962	0.82[YRI][hapmap]
rs7074629	0.81[AFR][1000 genomes]
rs7096359	0.87[ASW][hapmap];0.81[AFR][1000 genomes]
rs7919142	1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs9663346	0.81[AFR][1000 genomes];0.84[EUR][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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7089687	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112632800-112678000	Weak transcription	Lung	lung
2	chr10:112632800-112678200	Weak transcription	Spleen	Spleen
3	chr10:112633200-112656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:112633200-112656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:112633400-112662000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:112633600-112653800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:112633600-112655200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr10:112633800-112659800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:112634000-112649400	Weak transcription	Brain Hippocampus Middle	brain
10	chr10:112634000-112655000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr10:112634000-112655800	Weak transcription	Psoas Muscle	Psoas
12	chr10:112634000-112656000	Weak transcription	Right Ventricle	heart
13	chr10:112634000-112662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:112634200-112655800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:112634600-112656600	Weak transcription	NHEK	skin
16	chr10:112634800-112661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:112634800-112677400	Weak transcription	HUVEC	blood vessel
18	chr10:112635400-112657000	Strong transcription	HSMM	muscle
19	chr10:112635400-112661800	Strong transcription	Placenta	Placenta
20	chr10:112635600-112660600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:112635600-112662200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:112635600-112663400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr10:112635800-112647800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr10:112635800-112662200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:112636000-112652000	Strong transcription	Fetal Intestine Large	intestine
26	chr10:112636000-112664400	Strong transcription	Fetal Thymus	thymus
27	chr10:112636200-112656200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:112636400-112664800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr10:112637400-112656200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:112637600-112651000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr10:112638000-112648400	Strong transcription	NHDF-Ad	bronchial
32	chr10:112638200-112650600	Strong transcription	Adipose Nuclei	Adipose
33	chr10:112639200-112661000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:112639600-112647800	Strong transcription	Dnd41	blood
35	chr10:112640800-112647800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:112641000-112648400	Strong transcription	Hela-S3	cervix
37	chr10:112641800-112648000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:112641800-112655200	Weak transcription	Brain Angular Gyrus	brain
39	chr10:112642000-112647800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:112642200-112655000	Weak transcription	Aorta	Aorta
41	chr10:112643000-112667200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:112643400-112648000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:112643400-112648600	Strong transcription	HMEC	breast
44	chr10:112643400-112649400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:112643600-112648000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:112643600-112650400	Strong transcription	Fetal Kidney	kidney
47	chr10:112643800-112647800	Strong transcription	Primary B cells from cord blood	blood
48	chr10:112644000-112647800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr10:112644000-112647800	Strong transcription	Fetal Lung	lung
50	chr10:112644000-112648000	Genic enhancers	Primary T cells from cord blood	blood

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