Variant report

Variant	rs2501617
Chromosome Location	chr1:179960369-179960370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179923781..179925306-chr1:179959371..179960994,2	K562	blood:
2	chr1:179959937..179962261-chr1:179974244..179975764,2	K562	blood:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10753206	0.80[MEX][hapmap];0.86[TSI][hapmap]
rs10798729	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10798732	0.81[CEU][hapmap]
rs10913916	0.87[JPT][hapmap]
rs10913917	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913918	0.88[JPT][hapmap]
rs10913927	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12040314	0.81[CEU][hapmap]
rs12040376	0.80[CEU][hapmap]
rs1292777	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1297205	0.85[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1631932	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2477106	0.88[JPT][hapmap]
rs2477110	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2477111	0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477112	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477116	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477118	0.88[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2477119	0.87[JPT][hapmap]
rs2477120	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483621	0.96[EUR][1000 genomes]
rs2483622	0.88[JPT][hapmap]
rs2501607	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2501608	0.88[JPT][hapmap]
rs2501610	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501611	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501613	0.88[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2501615	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501616	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501620	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501621	0.88[JPT][hapmap]
rs2762859	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767200	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3767202	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3818999	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3930305	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4076449	0.88[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147169	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4256775	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4263962	0.82[CHB][hapmap]
rs4336810	0.81[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs4506429	0.81[CEU][hapmap]
rs4651054	0.86[EUR][1000 genomes]
rs4651057	0.80[EUR][1000 genomes]
rs4652457	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652462	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652463	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4652465	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4652470	0.82[TSI][hapmap]
rs4652471	0.81[CEU][hapmap]
rs483307	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs498625	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500371	0.81[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510209	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526683	0.80[JPT][hapmap]
rs528350	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533795	0.82[EUR][1000 genomes]
rs534168	0.85[CEU][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6425603	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425609	0.88[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs6657347	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6660984	0.81[JPT][hapmap]
rs6691435	0.80[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7524849	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551181	0.84[CEU][hapmap]
rs9286932	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425481	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425482	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425485	0.81[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs9425849	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425851	0.85[EUR][1000 genomes]
rs9425854	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425855	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425856	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425859	0.82[JPT][hapmap]
rs9425860	0.81[ASN][1000 genomes]
rs9425861	0.94[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425868	0.81[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2501617	ASTN1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179926800-179961400	Weak transcription	A549	lung
3	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:179938600-179965800	Weak transcription	Esophagus	oesophagus
6	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
7	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:179938600-179984600	Weak transcription	Lung	lung
9	chr1:179939000-179989000	Weak transcription	Gastric	stomach
10	chr1:179939800-179974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:179940000-179961200	Weak transcription	HSMM	muscle
12	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
13	chr1:179946400-179963200	Weak transcription	HUVEC	blood vessel
14	chr1:179946400-179965600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:179946400-179972800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:179946600-179961200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:179946600-179961400	Weak transcription	HepG2	liver
20	chr1:179946600-179965800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:179946600-179965800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:179946800-179963800	Weak transcription	Adipose Nuclei	Adipose
24	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
25	chr1:179948000-179961200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:179948400-179965800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:179948400-179971800	Weak transcription	Fetal Heart	heart
28	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:179949200-179961200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:179949200-179963800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:179950200-179966000	Weak transcription	Fetal Brain Female	brain
34	chr1:179951400-179972200	Weak transcription	Psoas Muscle	Psoas
35	chr1:179951400-179974600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:179951800-179974800	Weak transcription	Hela-S3	cervix
37	chr1:179952400-179965600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:179953400-179965400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:179953600-179964800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:179953600-179965800	Weak transcription	Brain Substantia Nigra	brain
41	chr1:179953600-179971400	Weak transcription	HMEC	breast
42	chr1:179953800-179965800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:179954200-179965800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:179954200-179975400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:179954600-179967000	Strong transcription	Fetal Thymus	thymus
46	chr1:179954600-179975600	Weak transcription	Fetal Kidney	kidney
47	chr1:179954800-179971200	Weak transcription	NHEK	skin
48	chr1:179955000-179989200	Weak transcription	Aorta	Aorta
49	chr1:179955200-179961000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:179955200-179961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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