Variant report

Variant	rs12024880
Chromosome Location	chr1:155908910-155908911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155907299-155917579	U87	brain:	n/a	n/a
2	POLR2A	chr1:155907227-155909074	U87	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155908071..155911067-chr1:155957605..155960580,2	K562	blood:
2	chr1:155908189..155909774-chr1:155948347..155950014,2	K562	blood:
3	chr1:155907837..155914260-chr1:155947632..155952579,11	MCF-7	breast:
4	chr1:155901745..155905224-chr1:155906395..155909651,4	MCF-7	breast:
5	chr1:155877559..155880207-chr1:155906771..155908937,2	MCF-7	breast:
6	chr1:155908146..155911427-chr1:155945545..155949380,5	K562	blood:
7	chr1:155908602..155911262-chr1:156012651..156014394,2	K562	blood:
8	chr1:155906562..155909421-chr1:155978385..155980354,2	K562	blood:
9	chr1:155906777..155910748-chr1:155946954..155949586,4	MCF-7	breast:
10	chr1:155908164..155910696-chr1:155960990..155962628,2	K562	blood:
11	chr1:155907911..155911148-chr1:155956540..155959636,3	MCF-7	breast:
12	chr1:155902651..155906027-chr1:155906064..155909646,10	K562	blood:

No data

Variant related genes	Relation type
RXFP4	TF binding region
KIAA0907	TF binding region
ENSG00000273002	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000224276	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11264422	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12027412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563627	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749405	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1749410	0.82[ASN][1000 genomes]
rs2993207	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4661151	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661175	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs488079	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490498	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs539602	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625658	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639398	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656247	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670523	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs729022	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7517204	0.82[ASN][1000 genomes]
rs7538214	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs822504	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822505	0.82[ASN][1000 genomes]
rs822508	0.82[ASN][1000 genomes]
rs822509	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs12024880	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155904800-155909200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:155904800-155910400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155904800-155911000	Weak transcription	Gastric	stomach
4	chr1:155905000-155909200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:155905000-155909400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:155905000-155909800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:155905000-155909800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:155905000-155909800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:155905000-155909800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:155905000-155909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:155905000-155909800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:155905000-155909800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:155905000-155909800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:155905000-155909800	Weak transcription	Colonic Mucosa	Colon
15	chr1:155905000-155909800	Weak transcription	Right Atrium	heart
16	chr1:155905000-155909800	Weak transcription	Spleen	Spleen
17	chr1:155905000-155909800	Weak transcription	K562	blood
18	chr1:155905000-155909800	Weak transcription	NHEK	skin
19	chr1:155905000-155910000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:155905000-155910000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:155905000-155910000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:155905000-155910000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:155905000-155910000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:155905000-155910000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:155905000-155910000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:155905000-155910000	Weak transcription	Esophagus	oesophagus
27	chr1:155905000-155910000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:155905000-155910000	Weak transcription	Stomach Mucosa	stomach
29	chr1:155905000-155910000	Weak transcription	NHLF	lung
30	chr1:155905000-155910200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:155905000-155910200	Weak transcription	Osteobl	bone
32	chr1:155905000-155910400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:155905000-155910400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:155905000-155910400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:155905000-155910400	Weak transcription	Fetal Stomach	stomach
36	chr1:155905000-155910400	Weak transcription	NHDF-Ad	bronchial
37	chr1:155905000-155910600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:155905000-155910600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:155905000-155913000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:155905000-155914600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:155905000-155914600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:155905000-155915200	Weak transcription	Fetal Brain Female	brain
43	chr1:155905000-155915800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:155905000-155915800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:155905000-155916000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:155905000-155916200	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:155905200-155909600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:155905200-155909600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:155905200-155909600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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