Variant report

Variant	rs3820592
Chromosome Location	chr1:156006013-156006014
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	chr1:156004095..156006153-chr1:156009168..156012102,4	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1111102	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11486142	0.82[AMR][1000 genomes]
rs12128541	0.82[ASN][1000 genomes]
rs2095402	0.82[ASN][1000 genomes]
rs2297792	0.82[ASN][1000 genomes]
rs34444588	0.82[ASN][1000 genomes]
rs59781317	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427297	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72708238	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72708239	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7517202	0.82[ASN][1000 genomes]
rs915178	0.92[AMR][1000 genomes];0.83[EUR][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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3820592	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155990800-156006800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:155991000-156011600	Weak transcription	Colonic Mucosa	Colon
3	chr1:155991200-156006600	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:155991200-156006600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:155991200-156010800	Weak transcription	Fetal Heart	heart
6	chr1:155991200-156020000	Weak transcription	GM12878-XiMat	blood
7	chr1:155996000-156010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:155996200-156006200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:155996200-156006600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:155996200-156006600	Weak transcription	Fetal Lung	lung
11	chr1:155996200-156007600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:155996200-156008600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:155996200-156010800	Weak transcription	NHEK	skin
14	chr1:155996200-156011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:155996200-156019600	Weak transcription	HMEC	breast
16	chr1:155996200-156022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:155998200-156006400	Weak transcription	Fetal Brain Female	brain
18	chr1:155999800-156020000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:156000600-156009800	Weak transcription	HepG2	liver
20	chr1:156001200-156022400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:156002200-156006800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:156002400-156006200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:156002600-156009000	Weak transcription	Small Intestine	intestine
24	chr1:156002800-156006600	Weak transcription	Ovary	ovary
25	chr1:156002800-156006800	Weak transcription	HSMM	muscle
26	chr1:156002800-156007600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:156003000-156006800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:156003000-156007400	Weak transcription	NH-A	brain
29	chr1:156003200-156006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:156003200-156009600	Weak transcription	Esophagus	oesophagus
31	chr1:156003200-156012800	Weak transcription	NHLF	lung
32	chr1:156003400-156006600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:156003400-156010600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:156003600-156006800	Weak transcription	Hela-S3	cervix
35	chr1:156003600-156007000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:156003600-156010400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:156003800-156006600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:156003800-156010400	Weak transcription	HUVEC	blood vessel
39	chr1:156004000-156010600	Weak transcription	Brain Substantia Nigra	brain
40	chr1:156004200-156010600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:156004200-156012200	Weak transcription	Primary B cells from cord blood	blood
42	chr1:156004400-156006600	Weak transcription	Aorta	Aorta
43	chr1:156004400-156006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:156004400-156018600	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:156004600-156006600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:156004600-156010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:156004800-156017800	Weak transcription	Fetal Brain Male	brain
48	chr1:156005200-156022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:156005400-156008000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:156005400-156008800	Strong transcription	Placenta	Placenta

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