Variant report

Variant	rs6041947
Chromosome Location	chr20:1371792-1371793
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1351555..1355162-chr20:1371278..1374408,3	MCF-7	breast:
2	chr20:1368016..1369679-chr20:1370045..1371864,2	K562	blood:
3	chr20:1371233..1373934-chr20:1446935..1449162,2	K562	blood:
4	chr20:1304653..1308515-chr20:1369739..1375969,7	MCF-7	breast:
5	chr20:1307620..1309289-chr20:1370365..1373331,2	K562	blood:
6	chr20:1341583..1343596-chr20:1371067..1372610,2	K562	blood:
7	chr20:1356708..1360006-chr20:1370558..1373951,3	K562	blood:
8	chr20:1345564..1348128-chr20:1371036..1372870,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000088832	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000229728	Chromatin interaction
ENSG00000088833	Chromatin interaction
ENSG00000234684	Chromatin interaction

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

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

rs_ID	r²[population]
rs11087049	0.87[AMR][1000 genomes]
rs12626072	0.87[AMR][1000 genomes]
rs56377442	0.82[AMR][1000 genomes]
rs6041880	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6041970	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6041971	0.87[AMR][1000 genomes]
rs6041976	0.87[AMR][1000 genomes]
rs6131424	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6131443	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134845	0.87[AMR][1000 genomes]
rs6134846	0.87[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:127 , 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	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr20:1368000-1372000	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:1368800-1372000	Enhancers	Brain Substantia Nigra	brain
5	chr20:1369000-1371800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr20:1369000-1372000	Genic enhancers	Fetal Stomach	stomach
7	chr20:1369000-1372200	Genic enhancers	Fetal Lung	lung
8	chr20:1369000-1372400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:1369000-1373200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr20:1369000-1373200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr20:1369200-1371800	Enhancers	Esophagus	oesophagus
12	chr20:1369200-1372200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:1369200-1372200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr20:1369400-1371800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:1369600-1372000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr20:1369600-1372400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:1369800-1372000	Genic enhancers	K562	blood
18	chr20:1369800-1372200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:1369800-1372200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:1369800-1372400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:1369800-1372600	Enhancers	Fetal Heart	heart
22	chr20:1370000-1371800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:1370000-1371800	Genic enhancers	Spleen	Spleen
24	chr20:1370000-1371800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
25	chr20:1370000-1372000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr20:1370000-1372000	Enhancers	Stomach Mucosa	stomach
27	chr20:1370200-1372200	Genic enhancers	Placenta	Placenta
28	chr20:1370400-1372000	Enhancers	Small Intestine	intestine
29	chr20:1370400-1372000	Transcr. at gene 5' and 3'	HepG2	liver
30	chr20:1370400-1372200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
31	chr20:1370400-1372400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:1370600-1371800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:1370600-1371800	Enhancers	Liver	Liver
34	chr20:1370600-1371800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
35	chr20:1370600-1372200	Genic enhancers	Fetal Intestine Large	intestine
36	chr20:1370600-1372600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:1370600-1372600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr20:1370600-1373000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr20:1370800-1372200	Enhancers	Fetal Kidney	kidney
40	chr20:1370800-1372800	Enhancers	Gastric	stomach
41	chr20:1370800-1374000	Active TSS	Rectal Smooth Muscle	rectum
42	chr20:1371000-1373200	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr20:1371200-1371800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
44	chr20:1371200-1371800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr20:1371200-1371800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:1371200-1371800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr20:1371200-1371800	Transcr. at gene 5' and 3'	Lung	lung
48	chr20:1371200-1371800	Transcr. at gene 5' and 3'	Thymus	Thymus
49	chr20:1371200-1372000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr20:1371200-1372000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood

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