Variant report

Variant	rs6105140
Chromosome Location	chr20:1412831-1412832
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	chr20:1408022..1413976-chr20:1445856..1450713,7	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696447	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873522	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308086	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58194712	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109837	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497853	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124855	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs959813	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
3	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
4	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
5	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
9	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
10	chr20:1408600-1414400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
12	chr20:1408800-1414200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:1408800-1414400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:1408800-1415000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
23	chr20:1409600-1413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
25	chr20:1410200-1415000	Weak transcription	HMEC	breast
26	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
27	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:1410800-1413200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr20:1410800-1414600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr20:1411000-1414600	Weak transcription	K562	blood
31	chr20:1411000-1415000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr20:1411000-1415000	Weak transcription	Adipose Nuclei	Adipose
33	chr20:1411000-1415200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:1411000-1415200	Weak transcription	NHEK	skin
35	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
36	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
37	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr20:1411400-1415000	Weak transcription	Osteobl	bone
41	chr20:1411400-1415200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:1411400-1415200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr20:1411600-1415000	Weak transcription	NHDF-Ad	bronchial
44	chr20:1411800-1413600	Enhancers	Primary B cells from cord blood	blood
45	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
46	chr20:1412000-1413200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr20:1412000-1415000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:1412000-1415200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr20:1412200-1414400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr20:1412400-1414200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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