Variant report

Variant	rs822504
Chromosome Location	chr1:155857540-155857541
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	chr1:155855687..155857743-chr1:155879584..155881525,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143622	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11264422	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12024880	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12027412	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12563627	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1749405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1749410	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2993207	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4661151	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4661175	0.86[EUR][1000 genomes]
rs488079	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs490498	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs539602	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625658	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs639398	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs656247	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656737	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670523	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729022	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7517204	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7538214	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs822505	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs822508	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs822509	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	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
rs822504	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155831000-155862600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:155831000-155862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:155831000-155863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:155831200-155862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:155831400-155859000	Weak transcription	HUVEC	blood vessel
9	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
10	chr1:155837600-155863000	Weak transcription	Colonic Mucosa	Colon
11	chr1:155841400-155863000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
13	chr1:155842600-155863400	Weak transcription	Right Atrium	heart
14	chr1:155844000-155862200	Weak transcription	Lung	lung
15	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
16	chr1:155847000-155860200	Strong transcription	Fetal Brain Female	brain
17	chr1:155847200-155860200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:155847400-155860400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:155849000-155858000	Strong transcription	Brain Germinal Matrix	brain
21	chr1:155849400-155863000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:155849600-155862800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:155850000-155862800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:155850400-155862400	Weak transcription	Placenta	Placenta
25	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:155851400-155859800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:155851400-155862600	Weak transcription	Adipose Nuclei	Adipose
28	chr1:155851400-155862600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:155851400-155862800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:155851400-155863200	Weak transcription	Aorta	Aorta
31	chr1:155851400-155866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:155851400-155866000	Weak transcription	Spleen	Spleen
33	chr1:155851400-155866400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:155851400-155867400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:155851600-155859400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:155851600-155866800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:155851600-155870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:155852600-155862800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:155852600-155863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:155853000-155863400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:155853200-155862200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:155853200-155863000	Weak transcription	Left Ventricle	heart
43	chr1:155853600-155862800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:155854200-155862400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:155854200-155868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:155854400-155866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:155854400-155866400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:155854600-155858000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:155854600-155859000	Weak transcription	HSMM	muscle

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