Variant report

Variant	rs6109623
Chromosome Location	chr20:1346596-1346597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1346000..1350154-chr20:1350167..1354202,4	K562	blood:
2	chr20:1343841..1348695-chr20:1349294..1353469,5	K562	blood:
3	chr20:1345564..1348128-chr20:1371036..1372870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17718574	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4813115	0.86[ASW][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap]
rs6041420	0.86[MEX][hapmap]
rs6105031	0.93[ASW][hapmap];0.97[LWK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs6109605	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs6109740	0.93[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs733233	0.80[ASW][hapmap]
rs73581243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs747611	0.93[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1310000-1348800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:1323000-1350600	Weak transcription	Fetal Brain Male	brain
3	chr20:1323400-1354000	Weak transcription	Fetal Heart	heart
4	chr20:1326000-1350600	Weak transcription	Right Atrium	heart
5	chr20:1326800-1348200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:1331600-1349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:1331600-1358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr20:1332400-1348400	Weak transcription	Psoas Muscle	Psoas
10	chr20:1332400-1349200	Weak transcription	Colonic Mucosa	Colon
11	chr20:1333200-1349000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:1336200-1348000	Weak transcription	Aorta	Aorta
13	chr20:1336200-1348000	Weak transcription	Brain Germinal Matrix	brain
14	chr20:1336200-1348000	Weak transcription	Esophagus	oesophagus
15	chr20:1336200-1350600	Weak transcription	Right Ventricle	heart
16	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr20:1336400-1350600	Weak transcription	Fetal Lung	lung
18	chr20:1336400-1355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:1337600-1349400	Strong transcription	Fetal Muscle Leg	muscle
21	chr20:1337800-1348000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr20:1338400-1348000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:1338600-1354800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr20:1339000-1348800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr20:1339200-1348000	Weak transcription	Fetal Kidney	kidney
26	chr20:1339200-1348200	Weak transcription	Brain Angular Gyrus	brain
27	chr20:1339200-1348200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:1339200-1350600	Weak transcription	Pancreas	Pancrea
29	chr20:1340000-1349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr20:1340200-1349000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr20:1340200-1349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr20:1340600-1346600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:1341200-1347800	Weak transcription	Osteobl	bone
34	chr20:1341200-1348000	Weak transcription	Brain Hippocampus Middle	brain
35	chr20:1341200-1348000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr20:1341200-1350400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr20:1341200-1351000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr20:1341200-1351600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr20:1341400-1348000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr20:1341400-1348000	Weak transcription	Ovary	ovary
41	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
42	chr20:1341600-1348000	Weak transcription	Fetal Brain Female	brain
43	chr20:1341600-1350600	Weak transcription	Brain Substantia Nigra	brain
44	chr20:1341600-1350800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr20:1341800-1347800	Weak transcription	Placenta	Placenta
46	chr20:1341800-1350800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:1342200-1346800	Strong transcription	Fetal Stomach	stomach
48	chr20:1342400-1348000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr20:1342400-1349000	Weak transcription	Colon Smooth Muscle	Colon
50	chr20:1342600-1348200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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