Variant report

Variant	rs17373425
Chromosome Location	chr1:180642165-180642166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180600246..180602406-chr1:180641858..180644833,2	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11487432	0.88[EUR][1000 genomes]
rs12089469	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17301405	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17301581	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17301602	0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17301762	0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17301936	0.88[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17302040	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17373383	0.85[CEU][hapmap]
rs17373501	0.89[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17373660	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs59077359	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809307	0.81[EUR][1000 genomes]
rs61809308	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61809311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61809312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61809314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61809317	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809334	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809342	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809345	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809347	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809350	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809351	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809352	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61809353	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61809354	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61809355	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61809356	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61809357	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61809358	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811160	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811190	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811191	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811192	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811193	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811197	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811199	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811202	0.96[EUR][1000 genomes]
rs61811204	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811221	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811222	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61811223	0.92[EUR][1000 genomes]
rs61811224	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811225	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811227	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6664966	0.89[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674012	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6681637	0.92[EUR][1000 genomes]
rs6698414	0.81[EUR][1000 genomes]
rs72707419	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72721001	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72723004	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723006	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723010	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72723014	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72723023	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723026	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723027	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723035	0.96[EUR][1000 genomes]
rs72723043	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180645200	Weak transcription	Gastric	stomach
2	chr1:180631600-180644400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:180632200-180644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:180633200-180672000	Weak transcription	K562	blood
5	chr1:180633400-180642600	Weak transcription	Pancreas	Pancrea
6	chr1:180634000-180643400	Weak transcription	Left Ventricle	heart
7	chr1:180634800-180643800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:180635000-180642600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:180635000-180644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:180635200-180654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:180636400-180647200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:180636400-180651800	Weak transcription	Ovary	ovary
13	chr1:180640200-180643800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:180640200-180662200	Weak transcription	Fetal Heart	heart
15	chr1:180640600-180660600	Weak transcription	Right Ventricle	heart
16	chr1:180641000-180642200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:180641000-180653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:180641200-180642600	Weak transcription	Aorta	Aorta
19	chr1:180641200-180644000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:180641200-180644400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:180641200-180647400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:180641200-180653400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:180641200-180662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:180641400-180644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:180641600-180642400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:180641600-180661200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:180641800-180644800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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