Variant report

Variant	rs1490578
Chromosome Location	chr1:212660609-212660610
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212629922..212631691-chr1:212659895..212661692,2	K562	blood:
2	chr1:212654477..212657612-chr1:212658521..212662499,5	K562	blood:
3	chr1:212658367..212661601-chr1:212781233..212783647,4	MCF-7	breast:
4	chr1:212657982..212660814-chr1:212768286..212770089,2	K562	blood:
5	chr1:212648507..212667078-chr1:212779147..212787651,52	K562	blood:
6	chr1:212657477..212661646-chr1:212730263..212734721,4	K562	blood:
7	chr1:212660151..212661692-chr1:212667519..212669650,2	K562	blood:
8	chr1:212645024..212669819-chr1:212778382..212791615,68	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260805	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10779580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741983	0.80[YRI][hapmap];0.91[AFR][1000 genomes]
rs35431877	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951450	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523210	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611108	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618937	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665276	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7544479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791562	1.00[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
12	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212650600-212667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:212650800-212661600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:212655000-212665800	Enhancers	Placenta	Placenta
4	chr1:212655200-212662800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:212655600-212662200	Weak transcription	Right Atrium	heart
6	chr1:212656400-212661600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:212656400-212661600	Weak transcription	Aorta	Aorta
8	chr1:212656400-212662000	Weak transcription	Left Ventricle	heart
9	chr1:212656800-212661400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:212656800-212661800	Weak transcription	Colonic Mucosa	Colon
11	chr1:212656800-212662200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:212657200-212664800	Weak transcription	Spleen	Spleen
13	chr1:212658000-212662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:212658000-212663000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:212658000-212663000	Enhancers	Stomach Mucosa	stomach
16	chr1:212658200-212663000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:212659200-212660800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:212659200-212661000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:212659400-212661600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:212659400-212661600	Weak transcription	Brain Anterior Caudate	brain
21	chr1:212659600-212661400	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:212659600-212661600	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:212659600-212662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:212659600-212662000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:212659800-212661000	Enhancers	HepG2	liver
26	chr1:212659800-212661400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:212659800-212661600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:212659800-212661800	Weak transcription	GM12878-XiMat	blood
29	chr1:212660000-212661000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:212660000-212661200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:212660000-212661400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:212660000-212661400	Enhancers	A549	lung
33	chr1:212660000-212661400	Weak transcription	HSMMtube	muscle
34	chr1:212660000-212661600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:212660000-212661600	Weak transcription	HSMM	muscle
36	chr1:212660000-212661600	Weak transcription	K562	blood
37	chr1:212660000-212661600	Weak transcription	NHEK	skin
38	chr1:212660000-212662000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:212660000-212662200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:212660000-212662200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:212660000-212662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:212660000-212662200	Weak transcription	NHDF-Ad	bronchial
43	chr1:212660000-212662400	Weak transcription	Esophagus	oesophagus
44	chr1:212660000-212664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:212660200-212661200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:212660200-212661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:212660200-212661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:212660200-212661400	Weak transcription	Fetal Intestine Large	intestine
49	chr1:212660200-212661400	Weak transcription	Fetal Intestine Small	intestine
50	chr1:212660200-212661400	Weak transcription	Monocytes-CD14+_RO01746	blood

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