Variant report

Variant	rs589780
Chromosome Location	chr1:179845022-179845023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
2	chr1:179844647..179846808-chr1:180163421..180165631,2	K562	blood:
3	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
4	chr1:179844379..179846987-chr1:180122185..180123975,2	MCF-7	breast:
5	chr1:179840648..179843448-chr1:179843849..179845352,2	MCF-7	breast:
6	chr1:179834118..179836947-chr1:179843310..179847312,3	MCF-7	breast:
7	chr1:179832603..179840385-chr1:179843229..179848672,10	MCF-7	breast:
8	chr1:179844894..179847778-chr1:180122782..180124340,2	K562	blood:
9	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL359853.2-1	chr1:179842841-179845312	NONHSAT008224

No data

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000258664	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1014394	0.82[EUR][1000 genomes]
rs1144575	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1148812	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1148815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148817	0.81[EUR][1000 genomes]
rs12062341	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12062383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1281410	0.82[EUR][1000 genomes]
rs1281411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281412	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281413	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281428	0.93[ASN][1000 genomes]
rs1281429	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281430	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281432	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1298477	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1298479	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1299684	0.81[YRI][hapmap]
rs1300068	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245425	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762858	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777908	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777909	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777917	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2794582	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2794583	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474258	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475233	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475434	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479094	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs480498	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs486906	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs501300	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502036	0.84[AMR][1000 genomes]
rs505789	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs514421	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522534	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530369	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs530854	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531814	0.81[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs538512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547776	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549650	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555526	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600046	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600553	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs605807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612215	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs615337	0.80[AMR][1000 genomes]
rs644412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	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
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
2	chr1:179828000-179845600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:179830200-179845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:179835000-179845600	Weak transcription	Ovary	ovary
5	chr1:179835000-179846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:179835000-179846400	Weak transcription	Spleen	Spleen
7	chr1:179835200-179845200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:179835200-179845600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:179835400-179846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:179836600-179845400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:179837000-179845600	Weak transcription	Aorta	Aorta
12	chr1:179837200-179845400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:179837400-179845400	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:179837600-179845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:179838200-179845800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:179838200-179846000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:179838200-179846200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:179838400-179845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:179839000-179845200	Weak transcription	Fetal Brain Female	brain
20	chr1:179840400-179845600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:179840600-179845200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:179841400-179845200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:179841600-179846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:179842000-179845200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:179842600-179845200	Weak transcription	Right Atrium	heart
26	chr1:179843400-179845200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:179843600-179845200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:179843600-179845400	Weak transcription	NHDF-Ad	bronchial
29	chr1:179843800-179845400	Weak transcription	Thymus	Thymus
30	chr1:179843800-179845600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:179843800-179845600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:179843800-179845800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:179843800-179846200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:179843800-179846200	Weak transcription	Lung	lung
35	chr1:179844000-179845200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:179844000-179846200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:179844200-179845200	Weak transcription	Colonic Mucosa	Colon
38	chr1:179844200-179845200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:179844200-179845400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:179844200-179845800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:179844200-179846000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:179844200-179846000	Weak transcription	Fetal Thymus	thymus
43	chr1:179844200-179846200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:179844400-179845200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:179844400-179845400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:179844400-179845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr1:179844400-179846000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:179844400-179846200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:179844400-179846200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:179844400-179846200	Weak transcription	Left Ventricle	heart

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