Variant report

Variant	rs57939520
Chromosome Location	chr1:78288885-78288886
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78285341..78286851-chr1:78287650..78290404,2	K562	blood:
2	chr1:78287859..78289541-chr1:78464426..78466879,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs56140793	1.00[AMR][1000 genomes]
rs59090864	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59272007	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59814571	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6689686	1.00[AMR][1000 genomes]
rs74090656	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74090677	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74090699	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74092307	1.00[AMR][1000 genomes]
rs74092311	1.00[AMR][1000 genomes]
rs74092330	0.81[AFR][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	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
2	chr1:78266000-78298000	Weak transcription	K562	blood
3	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
5	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:78273400-78289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:78273600-78290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:78273600-78290000	Weak transcription	Psoas Muscle	Psoas
9	chr1:78273600-78293200	Weak transcription	Brain Germinal Matrix	brain
10	chr1:78274600-78290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:78274800-78297400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:78274800-78297600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:78274800-78298000	Weak transcription	Fetal Kidney	kidney
14	chr1:78275000-78289000	Weak transcription	A549	lung
15	chr1:78275000-78312800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:78277000-78290200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:78277400-78291200	Strong transcription	Fetal Intestine Small	intestine
18	chr1:78277600-78292600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:78278400-78289600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:78278800-78290200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:78279200-78289600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:78279200-78300400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:78279400-78289600	Strong transcription	Fetal Thymus	thymus
24	chr1:78279400-78289800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:78279400-78290600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:78279800-78294800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:78280000-78292200	Weak transcription	Aorta	Aorta
28	chr1:78280400-78289400	Weak transcription	NHLF	lung
29	chr1:78280400-78297400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:78280600-78291000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:78280600-78292600	Weak transcription	Lung	lung
32	chr1:78280600-78298000	Weak transcription	Fetal Brain Male	brain
33	chr1:78280600-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:78281000-78291600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:78281000-78296600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:78281000-78308800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:78281200-78290200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:78281200-78316400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:78281600-78297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:78282800-78293600	Strong transcription	Dnd41	blood
41	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:78283000-78289600	Weak transcription	Hela-S3	cervix
43	chr1:78283000-78291000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:78283200-78289600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:78283200-78296600	Weak transcription	Right Ventricle	heart
46	chr1:78283400-78289800	Weak transcription	NHEK	skin
47	chr1:78283400-78292600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:78283600-78295000	Weak transcription	Left Ventricle	heart
49	chr1:78284200-78290200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:78284400-78289600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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