Variant report

Variant	rs780382
Chromosome Location	chr11:9881475-9881476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10840314	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042524	0.82[ASW][hapmap];0.87[LWK][hapmap];0.82[AFR][1000 genomes]
rs2649049	0.82[JPT][hapmap]
rs360159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360165	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs360167	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7124727	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs780381	0.96[ASN][1000 genomes]
rs7929434	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7943244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking 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	40 gene(s)	inside rSNPs	diseases
2	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs780382	ZCCHC24	trans	cerebellum	SCAN
rs780382	SWAP70	cis	parietal	SCAN
rs780382	OR52E6	cis	parietal	SCAN
rs780382	ASCL3	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
2	chr11:9863800-9883800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:9868600-9883400	Weak transcription	HSMMtube	muscle
4	chr11:9876600-9882800	Enhancers	Osteobl	bone
5	chr11:9877600-9890200	Weak transcription	Brain Anterior Caudate	brain
6	chr11:9877800-9897000	Weak transcription	Psoas Muscle	Psoas
7	chr11:9878200-9883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:9878200-9883800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:9878200-9884000	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:9878200-9884600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:9878200-9892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:9878200-9897000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:9878400-9883400	Weak transcription	HMEC	breast
14	chr11:9878400-9883400	Weak transcription	NHEK	skin
15	chr11:9878400-9891800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:9878400-9893200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:9878400-9916200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:9878600-9882000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:9878800-9881600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr11:9878800-9881600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr11:9878800-9881600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr11:9878800-9881800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:9878800-9882200	Enhancers	NHLF	lung
24	chr11:9878800-9883600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
26	chr11:9879000-9882000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:9879000-9882400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:9879200-9886000	Enhancers	NHDF-Ad	bronchial
29	chr11:9879400-9881800	Enhancers	Primary hematopoietic stem cells	blood
30	chr11:9879400-9882400	Enhancers	Primary T cells from cord blood	blood
31	chr11:9879600-9881600	Enhancers	Dnd41	blood
32	chr11:9879600-9881800	Enhancers	Fetal Lung	lung
33	chr11:9879600-9882000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:9879600-9882000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr11:9879600-9882000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:9879600-9882600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:9879800-9881600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:9879800-9881600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr11:9879800-9881600	Enhancers	NH-A	brain
40	chr11:9879800-9881800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr11:9879800-9881800	Enhancers	HSMM	muscle
42	chr11:9879800-9882000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:9879800-9882200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr11:9880000-9881600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:9880000-9881600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:9880000-9881600	Enhancers	Fetal Kidney	kidney
47	chr11:9880000-9891600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr11:9880200-9913200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr11:9880600-9881600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:9880600-9882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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