Variant report

Variant	rs3802481
Chromosome Location	chr9:14618668-14618669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10756585	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756586	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs10810186	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810188	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810190	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10810191	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810196	0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810199	0.83[YRI][hapmap]
rs10810202	0.87[YRI][hapmap]
rs10961593	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10961596	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10961597	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10961599	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10961605	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10961610	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10961616	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961619	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10961621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10961640	0.80[CHB][hapmap]
rs12237470	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683789	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4278237	0.88[CHB][hapmap]
rs4298581	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59010612	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7045207	0.87[EUR][1000 genomes]
rs7048089	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73405730	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7853156	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv471285	chr9:14589173-14622952	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv892607	chr9:14589173-14622952	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv892608	chr9:14589173-14689088	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv892609	chr9:14589173-14694302	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv613641	chr9:14590805-14622952	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv613642	chr9:14592180-14639666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv2752921	chr9:14593749-14694372	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2755661	chr9:14615367-14660700	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802481	ZDHHC21	cis	multi-tissue	Pritchard
rs3802481	ENSG00000175893	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14586800-14629800	Weak transcription	Primary T cells from cord blood	blood
2	chr9:14588200-14618800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:14594800-14633400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:14595600-14653600	Weak transcription	NHDF-Ad	bronchial
5	chr9:14596600-14618800	Weak transcription	Left Ventricle	heart
6	chr9:14596600-14618800	Weak transcription	Ovary	ovary
7	chr9:14596600-14618800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:14596600-14627200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:14596600-14627600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:14596600-14629600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:14596600-14629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:14596600-14630600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:14596600-14630600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:14596600-14630800	Weak transcription	Aorta	Aorta
15	chr9:14596600-14630800	Weak transcription	Fetal Intestine Small	intestine
16	chr9:14596600-14630800	Weak transcription	HSMMtube	muscle
17	chr9:14596600-14634000	Weak transcription	Gastric	stomach
18	chr9:14596600-14653600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:14597000-14618800	Weak transcription	Fetal Intestine Large	intestine
20	chr9:14597000-14655000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:14597800-14633600	Weak transcription	Pancreas	Pancrea
22	chr9:14598200-14620800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:14598200-14633200	Weak transcription	Fetal Stomach	stomach
24	chr9:14599800-14654000	Weak transcription	Fetal Heart	heart
25	chr9:14601400-14636800	Weak transcription	Small Intestine	intestine
26	chr9:14604600-14631000	Weak transcription	GM12878-XiMat	blood
27	chr9:14605600-14630000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:14605600-14654800	Weak transcription	HSMM	muscle
29	chr9:14605800-14634000	Weak transcription	Esophagus	oesophagus
30	chr9:14608400-14627000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:14609600-14628200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:14610000-14627200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:14610200-14618800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:14610200-14654800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:14610400-14618800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:14611200-14632800	Weak transcription	Placenta	Placenta
37	chr9:14612400-14630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:14612800-14641200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:14613600-14654600	Weak transcription	Fetal Kidney	kidney
40	chr9:14613800-14618800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:14614800-14627600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:14615000-14618800	Weak transcription	Fetal Muscle Leg	muscle
43	chr9:14615000-14630800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:14615400-14619000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:14615400-14622400	Weak transcription	Primary B cells from cord blood	blood
46	chr9:14615800-14618800	Weak transcription	Lung	lung
47	chr9:14615800-14620600	Weak transcription	Stomach Mucosa	stomach
48	chr9:14616800-14619000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr9:14616800-14630400	Weak transcription	Fetal Brain Female	brain
50	chr9:14617000-14621400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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