Variant report

Variant	rs6041880
Chromosome Location	chr20:1364521-1364522
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	chr20:1355645..1357681-chr20:1363230..1365988,2	K562	blood:
2	chr20:1305375..1307860-chr20:1363586..1366109,2	K562	blood:

Variant related genes	Relation type
ENSG00000234684	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11087049	0.84[AMR][1000 genomes]
rs12626072	0.84[AMR][1000 genomes]
rs1323135	0.81[CHB][hapmap]
rs2317648	0.85[JPT][hapmap]
rs6041947	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6041970	0.84[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs6041971	0.85[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs6041976	0.84[AMR][1000 genomes]
rs6131424	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131443	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134693	0.85[CEU][hapmap]
rs6134845	0.84[AMR][1000 genomes]
rs6134846	0.84[AMR][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	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
4	chr20:1348000-1366800	Strong transcription	Dnd41	blood
5	chr20:1353200-1369400	Weak transcription	Brain Germinal Matrix	brain
6	chr20:1354400-1371200	Weak transcription	Fetal Brain Male	brain
7	chr20:1355400-1369000	Weak transcription	Fetal Brain Female	brain
8	chr20:1355600-1366400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr20:1355600-1369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:1356400-1365600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr20:1356400-1369600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1356600-1369800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:1356800-1365400	Weak transcription	Colonic Mucosa	Colon
14	chr20:1356800-1369200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr20:1357600-1369000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr20:1357800-1365800	Genic enhancers	HepG2	liver
18	chr20:1358000-1367000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr20:1358200-1369600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr20:1358400-1369800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr20:1358600-1366800	Weak transcription	Aorta	Aorta
22	chr20:1358600-1369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:1358800-1370000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr20:1359000-1366400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:1359000-1369000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:1359200-1369600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:1359600-1369800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr20:1360000-1369800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr20:1360000-1369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr20:1360200-1366400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr20:1360600-1367200	Enhancers	Stomach Mucosa	stomach
32	chr20:1361200-1369000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr20:1361800-1367600	Enhancers	Adipose Nuclei	Adipose
34	chr20:1362000-1367400	Genic enhancers	Primary T cells from cord blood	blood
35	chr20:1362400-1369000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr20:1362600-1364600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr20:1362600-1364800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr20:1362600-1367400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:1362600-1367600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr20:1362800-1364600	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr20:1362800-1364600	Enhancers	Left Ventricle	heart
42	chr20:1362800-1364800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr20:1362800-1364800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr20:1362800-1365200	Genic enhancers	GM12878-XiMat	blood
45	chr20:1362800-1365600	Enhancers	Pancreas	Pancrea
46	chr20:1362800-1365600	Genic enhancers	NHEK	skin
47	chr20:1362800-1367000	Enhancers	Psoas Muscle	Psoas
48	chr20:1362800-1368000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:1362800-1368200	Enhancers	Right Ventricle	heart
50	chr20:1363000-1364800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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