Variant report

Variant	rs17758404
Chromosome Location	chr2:184089822-184089823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17707306	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17707407	1.00[AFR][1000 genomes]
rs17707482	0.95[AFR][1000 genomes]
rs17707596	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17707626	1.00[AFR][1000 genomes]
rs17758051	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17758247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17758271	0.97[AFR][1000 genomes]
rs17758295	0.98[AFR][1000 genomes]
rs17758560	0.80[AFR][1000 genomes]
rs57461422	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58870754	0.92[AFR][1000 genomes]
rs59938270	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61058678	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62188082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62188083	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7601755	1.00[AFR][1000 genomes]
rs7603511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:49 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875486	chr2:184016627-184095979	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv3067	chr2:184079419-184119957	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv508187	chr2:184080265-184100539	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	esv2763254	chr2:184084153-184097520	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv999917	chr2:184084153-184102657	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv1011473	chr2:184084153-184104561	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
12	nsv1007287	chr2:184084153-184106849	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	nsv583921	chr2:184084221-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
14	nsv583922	chr2:184084221-184090844	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
15	nsv583923	chr2:184084221-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
16	esv3521246	chr2:184084557-184092055	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
17	esv3521244	chr2:184084857-184091955	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	esv3521248	chr2:184085171-184091187	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
19	esv3458827	chr2:184085394-184091071	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
20	esv3521242	chr2:184085429-184091058	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
21	esv3521243	chr2:184085439-184090988	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
22	nsv1014008	chr2:184085441-184111385	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
23	esv3521247	chr2:184085443-184091038	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
24	esv12332	chr2:184085446-184090996	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
25	esv3458828	chr2:184085448-184091038	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
26	esv2421754	chr2:184085453-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
27	esv3458826	chr2:184085453-184091044	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
28	esv3521245	chr2:184085469-184091002	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
29	esv3521250	chr2:184085474-184090997	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
30	esv3391210	chr2:184085489-184090972	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
31	esv3521249	chr2:184085518-184090956	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
32	esv3521251	chr2:184085520-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
33	esv3458829	chr2:184085522-184090954	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
34	nsv583929	chr2:184085788-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
35	nsv583930	chr2:184085788-184090844	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
36	nsv583931	chr2:184085788-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
37	nsv517040	chr2:184085788-184095979	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
38	nsv583932	chr2:184085788-184095979	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
39	nsv215031	chr2:184085889-184093428	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
40	nsv583937	chr2:184086214-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
41	nsv583938	chr2:184086214-184090844	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
42	nsv583939	chr2:184086214-184090947	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
43	nsv583943	chr2:184086289-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
44	nsv583944	chr2:184086289-184090844	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
45	nsv583945	chr2:184086289-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
46	nsv583948	chr2:184086397-184089822	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
47	nsv583949	chr2:184086397-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
48	nsv514106	chr2:184086555-184090571	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
49	nsv583950	chr2:184087428-184090947	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17758404	SIAH1	trans	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:184050400-184091600	Weak transcription	Psoas Muscle	Psoas
2	chr2:184072600-184094000	Weak transcription	HSMM	muscle
3	chr2:184082400-184091400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:184085200-184097000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:184087600-184094000	Weak transcription	HSMMtube	muscle
6	chr2:184089400-184090200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:184089400-184092400	Enhancers	Fetal Brain Male	brain
8	chr2:184089400-184093000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:184089600-184090000	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr2:184089600-184090000	Enhancers	Fetal Lung	lung
11	chr2:184089600-184090200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:184089600-184090200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:184089600-184090200	Enhancers	Fetal Brain Female	brain
14	chr2:184089600-184090200	Enhancers	Osteobl	bone
15	chr2:184089600-184090400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:184089600-184090400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:184089600-184093000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:184089800-184090000	Enhancers	Fetal Muscle Leg	muscle
19	chr2:184089800-184090200	Enhancers	Brain Angular Gyrus	brain
20	chr2:184089800-184090200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:184089800-184090200	Enhancers	Brain Substantia Nigra	brain
22	chr2:184089800-184090200	Enhancers	Skeletal Muscle Male	skeletal muscle

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