Variant report

Variant	rs733233
Chromosome Location	chr20:1342533-1342534
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1304778..1307427-chr20:1340796..1343484,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNPH-1	chr20:1342266-1342556	ENSG00000229728.1
2	lnc-SNPH-2	chr20:1341701-1342621	NONHSAT078102

Variant related genes	Relation type
ENSG00000234684	Chromatin interaction
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4813115	0.80[ASW][hapmap]
rs6109623	0.80[ASW][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs733233	FKBP1A	cis	multi-tissue	Pritchard
rs733233	MRPS26	cis	cerebellum	SCAN
rs733233	DEFB125	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr20:1336000-1343000	Weak transcription	Gastric	stomach
13	chr20:1336000-1343800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:1336200-1348000	Weak transcription	Aorta	Aorta
15	chr20:1336200-1348000	Weak transcription	Brain Germinal Matrix	brain
16	chr20:1336200-1348000	Weak transcription	Esophagus	oesophagus
17	chr20:1336200-1350600	Weak transcription	Right Ventricle	heart
18	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr20:1336400-1350600	Weak transcription	Fetal Lung	lung
20	chr20:1336400-1355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:1337000-1343000	Strong transcription	HUVEC	blood vessel
23	chr20:1337600-1343000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr20:1337600-1349400	Strong transcription	Fetal Muscle Leg	muscle
25	chr20:1337800-1348000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr20:1338000-1342800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr20:1338000-1343200	Strong transcription	Dnd41	blood
28	chr20:1338200-1343400	Strong transcription	Liver	Liver
29	chr20:1338200-1344200	Strong transcription	Fetal Intestine Large	intestine
30	chr20:1338200-1344800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr20:1338400-1343400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr20:1338400-1344400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr20:1338400-1345000	Strong transcription	HepG2	liver
34	chr20:1338400-1348000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:1338600-1343600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr20:1338600-1344200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr20:1338600-1344400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr20:1338600-1345000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr20:1338600-1346400	Strong transcription	NHEK	skin
40	chr20:1338600-1354800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr20:1338800-1343800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr20:1338800-1344800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr20:1339000-1342600	Strong transcription	HSMM	muscle
44	chr20:1339000-1348800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:1339200-1343000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr20:1339200-1343400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr20:1339200-1344400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr20:1339200-1348000	Weak transcription	Fetal Kidney	kidney
49	chr20:1339200-1348200	Weak transcription	Brain Angular Gyrus	brain
50	chr20:1339200-1348200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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