Variant report

Variant	rs10793621
Chromosome Location	chr10:46122794-46122795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10793618	0.81[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1080264	0.81[CEU][hapmap];0.97[CHD][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10900227	0.90[CEU][hapmap]
rs11239558	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239559	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239564	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239565	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239567	0.86[CHB][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11239570	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239577	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11239585	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239587	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11528544	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12217545	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766066	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565096	0.83[EUR][1000 genomes]
rs1565097	0.80[EUR][1000 genomes]
rs1982794	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1982795	0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994426	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740107	0.81[EUR][1000 genomes]
rs3824617	0.87[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4948673	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4949003	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7074524	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095806	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73289207	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7900810	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900977	0.86[EUR][1000 genomes]
rs7918454	0.90[CEU][hapmap];0.93[CHD][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv947911	chr10:46116371-46136816	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10793621	AGAP4	cis	Artery Tibial	GTEx
rs10793621	ZFAND4	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46096200-46142000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:46098200-46153400	Weak transcription	HSMM	muscle
4	chr10:46100200-46142600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:46103400-46130600	Weak transcription	Fetal Brain Male	brain
6	chr10:46103400-46142200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr10:46103600-46132600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:46103800-46134600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:46105600-46141600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:46105800-46123800	Weak transcription	NHEK	skin
12	chr10:46106400-46137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:46106400-46141400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:46106400-46142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr10:46106800-46128000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr10:46106800-46142000	Weak transcription	Fetal Kidney	kidney
17	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:46107000-46125600	Weak transcription	Fetal Brain Female	brain
19	chr10:46107800-46141800	Weak transcription	Colon Smooth Muscle	Colon
20	chr10:46107800-46142000	Weak transcription	Esophagus	oesophagus
21	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
22	chr10:46108200-46142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:46108400-46122800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:46108400-46123000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr10:46108400-46142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:46108600-46123200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr10:46108600-46149200	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
31	chr10:46108800-46142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:46110200-46153800	Weak transcription	NH-A	brain
33	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:46112200-46152400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:46116400-46123200	Strong transcription	Primary T cells from cord blood	blood
36	chr10:46118800-46142400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:46119600-46122800	Strong transcription	Fetal Intestine Large	intestine
38	chr10:46119800-46137000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr10:46119800-46148200	Weak transcription	Colonic Mucosa	Colon
40	chr10:46120000-46122800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr10:46120200-46148400	Weak transcription	Small Intestine	intestine
43	chr10:46120800-46125000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:46120800-46126400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:46121000-46123200	Enhancers	Liver	Liver
46	chr10:46121000-46123400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr10:46121000-46125000	Strong transcription	Primary B cells from cord blood	blood
48	chr10:46121200-46123600	Strong transcription	Fetal Thymus	thymus
49	chr10:46121400-46123200	Strong transcription	Adipose Nuclei	Adipose
50	chr10:46121400-46123400	Strong transcription	Primary T cells fromperipheralblood	blood

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