Variant report

Variant	rs3777275
Chromosome Location	chr5:9169940-9169941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10462651	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10462863	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10513010	0.89[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10513011	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs11746238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479650	0.80[CEU][hapmap]
rs1806084	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1806088	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1806093	0.84[AMR][1000 genomes]
rs3797920	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797927	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846575	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757445	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv880683	chr5:9091164-9170323	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777275	CARD9	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
3	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:9152400-9171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:9153800-9183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:9154800-9170200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:9154800-9173400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:9154800-9176200	Weak transcription	Fetal Intestine Small	intestine
10	chr5:9154800-9176400	Weak transcription	Aorta	Aorta
11	chr5:9155000-9174200	Weak transcription	Liver	Liver
12	chr5:9156800-9171400	Weak transcription	Fetal Stomach	stomach
13	chr5:9157600-9176400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:9162200-9172000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:9163800-9189200	Weak transcription	Fetal Heart	heart
16	chr5:9164600-9170200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:9165200-9185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:9165600-9170400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:9165600-9170400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:9166400-9170000	Enhancers	Brain Germinal Matrix	brain
21	chr5:9166600-9176800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:9167800-9170200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:9168000-9171000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:9168400-9171800	Weak transcription	Left Ventricle	heart
25	chr5:9168600-9171200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:9168800-9170000	Enhancers	Fetal Lung	lung
27	chr5:9168800-9170400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:9168800-9170400	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:9168800-9170600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:9168800-9170800	Enhancers	HMEC	breast
31	chr5:9168800-9170800	Enhancers	NHDF-Ad	bronchial
32	chr5:9168800-9171000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:9168800-9171000	Enhancers	NHEK	skin
34	chr5:9168800-9171600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:9168800-9179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:9169000-9170000	Enhancers	Stomach Mucosa	stomach
37	chr5:9169000-9170000	Enhancers	Dnd41	blood
38	chr5:9169000-9170000	Enhancers	NHLF	lung
39	chr5:9169000-9170600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:9169000-9170800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:9169400-9170400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr5:9169400-9173600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:9169400-9173800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:9169400-9184600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:9169600-9170000	Weak transcription	Osteobl	bone
46	chr5:9169600-9171000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr5:9169800-9170000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:9169800-9173600	Weak transcription	NH-A	brain
49	chr5:9169800-9202800	Weak transcription	Duodenum Mucosa	Duodenum

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