Variant report

Variant	rs6138635
Chromosome Location	chr20:25658484-25658485
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	chr20:25652247..25655467-chr20:25656048..25658706,3	MCF-7	breast:
2	chr20:25650621..25655076-chr20:25655706..25658841,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-1	chr20:25654488-25658710	ENSG00000213742.2

Variant related genes	Relation type
ENSG00000236542	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs242121	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242123	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242127	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242128	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400630	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403424	1.00[ASN][1000 genomes]
rs6037154	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050691	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73111297	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73111300	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113113	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25651600-25659600	Strong transcription	Fetal Brain Female	brain
2	chr20:25652000-25659600	Strong transcription	Brain Germinal Matrix	brain
3	chr20:25652600-25658800	Strong transcription	Fetal Stomach	stomach
4	chr20:25653000-25663600	Strong transcription	HSMM	muscle
5	chr20:25653200-25659600	Strong transcription	Fetal Intestine Small	intestine
6	chr20:25653200-25662800	Strong transcription	Fetal Lung	lung
7	chr20:25653400-25658600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:25653400-25658800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr20:25653400-25659200	Strong transcription	Primary hematopoietic stem cells	blood
10	chr20:25653400-25659400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr20:25653400-25659600	Strong transcription	Brain Angular Gyrus	brain
12	chr20:25653400-25659600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr20:25653400-25659600	Strong transcription	Ovary	ovary
14	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr20:25653400-25661000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:25653400-25662400	Strong transcription	Liver	Liver
18	chr20:25653400-25663600	Strong transcription	Dnd41	blood
19	chr20:25653400-25664200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr20:25653600-25658600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:25653600-25658800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:25653600-25658800	Strong transcription	Rectal Smooth Muscle	rectum
23	chr20:25653600-25659000	Strong transcription	Brain Hippocampus Middle	brain
24	chr20:25653600-25659600	Strong transcription	Primary T cells from cord blood	blood
25	chr20:25653600-25659600	Strong transcription	Fetal Intestine Large	intestine
26	chr20:25653600-25659600	Strong transcription	Fetal Muscle Leg	muscle
27	chr20:25653600-25659600	Strong transcription	Fetal Thymus	thymus
28	chr20:25653600-25659600	Strong transcription	Left Ventricle	heart
29	chr20:25653600-25660000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr20:25653600-25660200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr20:25653600-25662600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr20:25653600-25663200	Strong transcription	HepG2	liver
33	chr20:25653800-25658600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr20:25653800-25659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr20:25653800-25659600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:25653800-25659600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr20:25653800-25664200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr20:25654000-25658800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr20:25654000-25659600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr20:25654000-25659600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr20:25654000-25659600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr20:25654000-25662600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:25654000-25663800	Weak transcription	Small Intestine	intestine
44	chr20:25654200-25659600	Strong transcription	Thymus	Thymus
45	chr20:25654400-25659600	Strong transcription	Lung	lung
46	chr20:25654600-25658600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr20:25654600-25658800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr20:25655000-25658600	Strong transcription	GM12878-XiMat	blood
49	chr20:25655000-25661400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr20:25655200-25659000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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