Variant report

Variant	rs1961795
Chromosome Location	chr20:52826759-52826760
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:49345330..49348251-chr20:52823191..52827147,4	MCF-7	breast:
2	chr20:52824721..52826787-chr20:55839394..55842032,3	MCF-7	breast:
3	chr20:52826695..52829423-chr20:53117360..53120091,2	MCF-7	breast:
4	chr20:52824614..52827050-chrX:153713627..153715899,2	MCF-7	breast:
5	chr17:57915224..57917032-chr20:52824163..52827087,2	MCF-7	breast:
6	chr20:52816101..52817074-chr20:52825780..52826823,3	MCF-7	breast:
7	chr16:765349..767993-chr20:52824649..52827443,2	MCF-7	breast:
8	chr12:120727996..120730746-chr20:52824489..52827020,3	MCF-7	breast:
9	chr17:56735044..56737047-chr20:52822984..52826992,5	MCF-7	breast:
10	chr20:52825632..52827601-chr20:53272621..53275494,2	MCF-7	breast:
11	chr20:52825165..52826866-chr6:115066329..115069326,2	MCF-7	breast:
12	chr20:52824488..52827444-chr3:64007659..64009363,3	MCF-7	breast:
13	chr20:52826556..52827403-chr8:38759473..38760087,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000103260	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000163636	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11483554	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12479602	1.00[ASN][1000 genomes]
rs12624322	0.94[ASN][1000 genomes]
rs12624646	0.90[ASN][1000 genomes]
rs12625916	0.94[ASN][1000 genomes]
rs1418926	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418927	1.00[ASN][1000 genomes]
rs6023044	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6091836	0.97[ASN][1000 genomes]
rs62216577	0.97[ASN][1000 genomes]
rs62216585	0.87[ASN][1000 genomes]
rs7267971	0.81[ASN][1000 genomes]
rs7270114	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137408	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52825400-52826800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:52825400-52828400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:52825400-52829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:52825400-52838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr20:52825600-52826800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:52825600-52827000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr20:52825600-52827000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr20:52825600-52827200	Enhancers	Stomach Mucosa	stomach
9	chr20:52825600-52827400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:52825600-52833800	Weak transcription	Lung	lung
11	chr20:52825600-52839000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:52825800-52826800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:52825800-52826800	Enhancers	Primary T cells from cord blood	blood
14	chr20:52825800-52826800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr20:52825800-52826800	Enhancers	Fetal Muscle Leg	muscle
16	chr20:52825800-52826800	Enhancers	Fetal Stomach	stomach
17	chr20:52825800-52827000	Enhancers	Thymus	Thymus
18	chr20:52825800-52827200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr20:52825800-52831400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:52826000-52826800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr20:52826000-52826800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr20:52826000-52826800	Enhancers	Fetal Heart	heart
23	chr20:52826000-52826800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr20:52826000-52826800	Active TSS	Stomach Smooth Muscle	stomach
25	chr20:52826000-52827000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr20:52826000-52827000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:52826000-52827000	Enhancers	Fetal Lung	lung
28	chr20:52826000-52827000	Enhancers	Psoas Muscle	Psoas
29	chr20:52826000-52827000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr20:52826000-52827000	Enhancers	NHDF-Ad	bronchial
31	chr20:52826000-52827200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr20:52826000-52827200	Enhancers	Right Atrium	heart
33	chr20:52826000-52827400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr20:52826000-52827400	Enhancers	Ovary	ovary
35	chr20:52826000-52828400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr20:52826000-52828800	Weak transcription	Aorta	Aorta
37	chr20:52826000-52831200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr20:52826000-52831400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr20:52826000-52831400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:52826000-52833400	Weak transcription	Esophagus	oesophagus
41	chr20:52826000-52833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr20:52826000-52837200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr20:52826000-52837800	Weak transcription	Fetal Thymus	thymus
44	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
45	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr20:52826200-52826800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr20:52826200-52826800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr20:52826200-52826800	Enhancers	Brain Angular Gyrus	brain
49	chr20:52826200-52826800	Enhancers	Brain Cingulate Gyrus	brain
50	chr20:52826200-52826800	Enhancers	Brain Hippocampus Middle	brain

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