Variant report

Variant	rs3805535
Chromosome Location	chr5:146774592-146774593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10042298	0.93[CHB][hapmap]
rs10042993	0.99[EUR][1000 genomes]
rs10070932	0.81[MEX][hapmap]
rs10515581	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs10515582	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs10515583	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs10515586	0.87[TSI][hapmap]
rs10515587	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11167988	0.93[JPT][hapmap]
rs11167989	0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11951154	0.86[MEX][hapmap]
rs12513884	0.90[ASN][1000 genomes]
rs12514302	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12515377	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs12518250	0.93[CHB][hapmap]
rs12518292	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12520080	0.92[CHB][hapmap]
rs12520436	0.86[CHB][hapmap]
rs12651731	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs12653560	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs1432838	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1432839	0.81[ASN][1000 genomes]
rs1432853	0.80[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs1432854	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs1432855	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs1432856	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs1432857	0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs17106470	0.93[CHB][hapmap]
rs17106482	0.93[CHB][hapmap]
rs17106492	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs17106560	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs17106572	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs17106575	0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs17106590	0.81[ASN][1000 genomes]
rs17106592	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17106597	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17106606	0.86[ASN][1000 genomes]
rs17106607	0.86[ASN][1000 genomes]
rs17106679	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106682	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106683	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106686	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106688	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs17106689	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106690	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs17106698	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs17106701	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs17484444	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17550470	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17550902	0.86[TSI][hapmap]
rs2288800	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2288805	0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2288809	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2304043	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2304047	0.95[ASN][1000 genomes]
rs2400294	0.81[MEX][hapmap]
rs2895681	0.90[ASN][1000 genomes]
rs3213857	0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs3749721	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3792837	0.93[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs3792839	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792840	0.81[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792841	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792843	0.88[ASN][1000 genomes]
rs3792844	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs3792845	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs3792846	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs3805533	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3805534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3805538	0.89[ASN][1000 genomes]
rs3805539	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805540	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805542	0.80[ASN][1000 genomes]
rs3805543	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs3805544	0.84[ASN][1000 genomes]
rs3805545	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs3805546	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs3816012	0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4642416	0.90[ASN][1000 genomes]
rs4705165	0.81[MEX][hapmap]
rs4705166	0.81[MEX][hapmap]
rs61405762	0.81[ASN][1000 genomes]
rs6866421	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6877045	0.97[EUR][1000 genomes]
rs6877057	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs6891468	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs72833326	0.97[EUR][1000 genomes]
rs73262265	0.81[ASN][1000 genomes]
rs7714240	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs918797	0.81[MEX][hapmap]
rs918798	0.80[MEX][hapmap]
rs972302	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3805535	SPINK6	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146762800-146775600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:146762800-146775600	Weak transcription	Placenta	Placenta
3	chr5:146762800-146775600	Weak transcription	Left Ventricle	heart
4	chr5:146762800-146775600	Weak transcription	Right Ventricle	heart
5	chr5:146762800-146783400	Weak transcription	Pancreas	Pancrea
6	chr5:146762800-146784200	Weak transcription	Colonic Mucosa	Colon
7	chr5:146763000-146775000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:146763000-146775200	Weak transcription	Right Atrium	heart
9	chr5:146764400-146777400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:146766200-146775400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:146766200-146775800	Weak transcription	Lung	lung
12	chr5:146767400-146782200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
14	chr5:146768000-146784000	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:146768400-146775000	Weak transcription	Fetal Intestine Large	intestine
16	chr5:146768600-146783400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:146769000-146783000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr5:146770200-146784800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:146770400-146775000	Strong transcription	Ovary	ovary
25	chr5:146770400-146775600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:146770400-146777200	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr5:146770400-146779000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:146770400-146783000	Strong transcription	Fetal Muscle Leg	muscle
29	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
30	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:146770600-146781600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:146770600-146782000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:146770600-146782800	Weak transcription	Fetal Heart	heart
34	chr5:146770600-146783200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:146770600-146783400	Strong transcription	Fetal Stomach	stomach
36	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:146770800-146777000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:146771000-146775800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:146771000-146781600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:146771200-146775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:146771200-146775800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:146771600-146774600	Weak transcription	NHDF-Ad	bronchial
44	chr5:146771600-146786600	Weak transcription	Gastric	stomach
45	chr5:146771800-146777200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:146771800-146780800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr5:146771800-146782000	Strong transcription	NH-A	brain
48	chr5:146772000-146774800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:146772000-146775200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:146772000-146781400	Strong transcription	Colon Smooth Muscle	Colon

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