Variant report

Variant	rs57990560
Chromosome Location	chr10:49524506-49524507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49522636..49524628-chr10:49534736..49536666,2	K562	blood:
2	chr10:49523430..49525253-chr10:49550597..49552808,2	K562	blood:
3	chr10:49520506..49525716-chr10:49528736..49531606,6	K562	blood:
4	chr10:49518153..49519864-chr10:49521781..49524737,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11101311	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259267	1.00[ASN][1000 genomes]
rs17010433	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17697960	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17697978	1.00[ASN][1000 genomes]
rs17698002	1.00[ASN][1000 genomes]
rs17770456	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17770535	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17770554	1.00[ASN][1000 genomes]
rs1978997	1.00[ASN][1000 genomes]
rs35009243	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3730156	1.00[ASN][1000 genomes]
rs3730157	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4354648	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57115982	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838674	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838676	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838695	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838696	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61838706	0.86[EUR][1000 genomes]
rs61840551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840552	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840553	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840555	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs724124	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7478030	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49515600-49525600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:49515600-49541400	Weak transcription	Lung	lung
3	chr10:49516000-49524600	Weak transcription	Stomach Mucosa	stomach
4	chr10:49516000-49525400	Weak transcription	Left Ventricle	heart
5	chr10:49516000-49525600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:49516000-49525600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:49516400-49525400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:49516400-49525600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr10:49516400-49525600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:49516400-49525600	Weak transcription	Brain Anterior Caudate	brain
11	chr10:49516400-49526400	Weak transcription	Brain Substantia Nigra	brain
12	chr10:49516400-49528000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:49516400-49528600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:49516400-49535000	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:49516400-49538400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:49516400-49538800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:49516400-49541400	Weak transcription	Right Atrium	heart
18	chr10:49516400-49547200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:49516600-49525200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:49516600-49525400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:49516600-49538400	Weak transcription	Primary B cells from cord blood	blood
23	chr10:49516600-49538600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:49516600-49538600	Weak transcription	Fetal Stomach	stomach
25	chr10:49517600-49525400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:49517800-49544600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:49518000-49526800	Weak transcription	Gastric	stomach
28	chr10:49518000-49528800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:49518000-49536000	Weak transcription	Fetal Intestine Small	intestine
30	chr10:49518200-49527600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:49518200-49542200	Weak transcription	HSMM	muscle
32	chr10:49518400-49525400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:49518400-49525600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:49518400-49525600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:49518400-49525600	Weak transcription	NH-A	brain
36	chr10:49518400-49526000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:49518600-49538400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:49518800-49534400	Weak transcription	Brain Germinal Matrix	brain
39	chr10:49518800-49538600	Weak transcription	Fetal Intestine Large	intestine
40	chr10:49518800-49540600	Weak transcription	NHEK	skin
41	chr10:49518800-49542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:49518800-49544000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr10:49519000-49525600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:49519000-49530600	Weak transcription	Fetal Brain Male	brain
45	chr10:49519000-49538600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:49519000-49540200	Weak transcription	HMEC	breast
47	chr10:49519200-49525800	Weak transcription	Fetal Brain Female	brain
48	chr10:49519400-49529600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr10:49519400-49532200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:49520200-49549800	Weak transcription	HUVEC	blood vessel

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