Variant report

Variant	rs17484444
Chromosome Location	chr5:146776249-146776250
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10042993	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515586	1.00[ASW][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs10515587	0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17548933	0.94[MEX][hapmap]
rs17550470	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17550902	1.00[ASW][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs3805535	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6866421	0.94[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6877045	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6877057	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833326	0.98[AMR][1000 genomes];0.98[EUR][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
rs17484444	SPINK6	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146762800-146783400	Weak transcription	Pancreas	Pancrea
2	chr5:146762800-146784200	Weak transcription	Colonic Mucosa	Colon
3	chr5:146764400-146777400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:146767400-146782200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
6	chr5:146768000-146784000	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:146768600-146783400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:146769000-146783000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr5:146770200-146784800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:146770400-146777200	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr5:146770400-146779000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:146770400-146783000	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
19	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:146770600-146781600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:146770600-146782000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:146770600-146782800	Weak transcription	Fetal Heart	heart
23	chr5:146770600-146783200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:146770600-146783400	Strong transcription	Fetal Stomach	stomach
25	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:146770800-146777000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:146771000-146781600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:146771600-146786600	Weak transcription	Gastric	stomach
30	chr5:146771800-146777200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:146771800-146780800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr5:146771800-146782000	Strong transcription	NH-A	brain
33	chr5:146772000-146781400	Strong transcription	Colon Smooth Muscle	Colon
34	chr5:146772000-146782600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:146772400-146783800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:146772600-146778600	Strong transcription	Aorta	Aorta
37	chr5:146772600-146778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:146772600-146778800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr5:146772600-146779800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:146772600-146781400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:146772800-146778800	Strong transcription	HUVEC	blood vessel
42	chr5:146772800-146782400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr5:146772800-146783400	Weak transcription	Brain Substantia Nigra	brain
44	chr5:146772800-146795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:146773000-146778200	Weak transcription	Brain Angular Gyrus	brain
46	chr5:146773200-146778000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:146773400-146781000	Weak transcription	Psoas Muscle	Psoas
48	chr5:146773400-146784000	Weak transcription	Fetal Brain Male	brain
49	chr5:146773600-146788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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