Variant report

Variant	rs11818604
Chromosome Location	chr10:45473552-45473553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr10:45472735-45473657	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:45470953-45474705	HepG2	liver:	n/a	n/a
3	HEY1	chr10:45470947-45474495	HepG2	liver:	n/a	n/a
4	MYBL2	chr10:45470920-45474664	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:45471121-45474585	GM19193	blood:	n/a	n/a
6	CTCF	chr10:45473500-45473650	HepG2	liver:	n/a	n/a
7	JUND	chr10:45473141-45473622	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:45473271-45474480	IMR90	lung:	n/a	n/a
9	POLR2A	chr10:45470342-45475147	HepG2	liver:	n/a	n/a
10	POLR2A	chr10:45466844-45474598	HepG2	liver:	n/a	n/a
11	POLR2A	chr10:45471912-45474616	GM19099	blood:	n/a	n/a
12	MBD4	chr10:45470183-45474624	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:45469731-45474525	U87	brain:	n/a	n/a
14	POLR2A	chr10:45471794-45473610	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:45473213-45474630	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr10:45467323-45474612	GM12878	blood:	n/a	n/a
17	MAX	chr10:45472786-45474507	HepG2	liver:	n/a	chr10:45474367-45474377
18	CTCF	chr10:45473460-45473610	HEK293	kidney:	n/a	n/a
19	POLR2A	chr10:45473424-45474553	GM18951	blood:	n/a	n/a
20	POLR2A	chr10:45469911-45474623	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr10:45470919-45474450	HepG2	liver:	n/a	n/a
22	JUND	chr10:45470094-45473588	HepG2	liver:	n/a	chr10:45470475-45470484
23	GATA2	chr10:45473470-45473951	SH-SY5Y	brain:	n/a	chr10:45473724-45473740 chr10:45473729-45473736 chr10:45473727-45473737 chr10:45473729-45473736 chr10:45473727-45473736 chr10:45473729-45473736
24	RFX5	chr10:45473544-45474461	HepG2	liver:	n/a	n/a
25	EP300	chr10:45473425-45474834	HepG2	liver:	n/a	chr10:45474007-45474017
26	POLR2A	chr10:45470967-45474597	HepG2	liver:	n/a	n/a
27	CTCF	chr10:45473460-45473610	WERI-Rb-1	eye:	n/a	n/a
28	POLR2A	chr10:45473498-45473685	GM12878	blood:	n/a	n/a
29	HEY1	chr10:45470980-45474704	HepG2	liver:	n/a	n/a
30	POLR2A	chr10:45472073-45474626	K562	blood:	n/a	n/a
31	NFIC	chr10:45470963-45474781	HepG2	liver:	n/a	n/a
32	POLR2A	chr10:45469553-45474630	HUVEC	blood vessel:	n/a	n/a
33	TEAD4	chr10:45473541-45473911	K562	blood:	n/a	n/a
34	POLR2A	chr10:45466471-45475094	HepG2	liver:	n/a	n/a
35	CTCF	chr10:45473511-45473593	Kidney_OC	kidney:	n/a	n/a
36	GATA3	chr10:45473536-45473975	MCF-7	breast:	n/a	chr10:45473724-45473740 chr10:45473729-45473736 chr10:45473727-45473737 chr10:45473729-45473736 chr10:45473727-45473736 chr10:45473729-45473736
37	POLR2A	chr10:45471778-45473632	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr10:45473431-45474608	GM12891	blood:	n/a	n/a
39	EBF1	chr10:45473448-45474591	GM12878	blood:	n/a	n/a
40	CTCF	chr10:45473509-45473594	H1-hESC	embryonic stem cell:	n/a	n/a
41	CHD2	chr10:45469556-45474650	HepG2	liver:	n/a	n/a
42	CCNT2	chr10:45472492-45474606	K562	blood:	n/a	n/a
43	POLR2A	chr10:45466202-45474927	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr10:45470923-45474628	U87	brain:	n/a	n/a
45	POLR2A	chr10:45471750-45473760	GM12878	blood:	n/a	n/a
46	POLR2A	chr10:45468699-45474919	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:45471901-45474434	HepG2	liver:	n/a	n/a
48	MXI1	chr10:45471972-45474875	HepG2	liver:	n/a	n/a
49	USF2	chr10:45473494-45473610	HepG2	liver:	n/a	n/a
50	MAZ	chr10:45473441-45473566	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45472874..45476114-chr10:45485945..45489321,3	MCF-7	breast:
2	chr10:45472768..45475523-chr10:45475664..45479867,4	MCF-7	breast:
3	chr10:45424948..45427085-chr10:45472059..45474210,2	K562	blood:
4	chr10:45472874..45475868-chr10:45493532..45497096,3	K562	blood:
5	chr10:45469560..45475620-chr10:45475961..45481693,7	MCF-7	breast:
6	chr10:45472274..45474352-chr10:45475240..45477414,3	K562	blood:
7	chr10:45359058..45361978-chr10:45470827..45473686,2	K562	blood:
8	chr10:45452399..45456775-chr10:45472666..45475790,4	MCF-7	breast:
9	chr10:45445329..45447053-chr10:45471994..45473924,2	K562	blood:
10	chr10:45424948..45428447-chr10:45472059..45474990,3	K562	blood:

Variant related genes	Relation type
RASSF4	TF binding region
ENSG00000224812	Chromatin interaction
ENSG00000187783	Chromatin interaction
ENSG00000273363	Chromatin interaction
ENSG00000165511	Chromatin interaction
ENSG00000107551	Chromatin interaction
ENSG00000165512	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11818623	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740094	0.84[ASN][1000 genomes]
rs3740097	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740098	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758401	0.92[EUR][1000 genomes]
rs869156	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs882845	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883733	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs883734	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883735	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914700	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914701	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11818604	RASSF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45470600-45473600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:45470600-45473800	Enhancers	Fetal Thymus	thymus
3	chr10:45470600-45474000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:45470600-45474200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr10:45470800-45473600	Weak transcription	Fetal Kidney	kidney
6	chr10:45470800-45473800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr10:45470800-45473800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:45470800-45473800	Weak transcription	Fetal Brain Male	brain
9	chr10:45470800-45474000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:45470800-45474000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:45470800-45474400	Active TSS	Right Atrium	heart
12	chr10:45470800-45476400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:45470800-45477800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:45470800-45479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:45471200-45473600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:45471200-45473600	Transcr. at gene 5' and 3'	Right Ventricle	heart
17	chr10:45471200-45474000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr10:45471200-45474600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:45471400-45474000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr10:45471400-45474400	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
21	chr10:45471400-45476600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr10:45471600-45473600	Weak transcription	A549	lung
23	chr10:45471600-45473800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:45471600-45473800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr10:45471600-45473800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:45471600-45473800	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
27	chr10:45471600-45474000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:45471600-45476800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr10:45471800-45473600	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
30	chr10:45471800-45473600	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:45471800-45473600	Transcr. at gene 5' and 3'	Left Ventricle	heart
32	chr10:45471800-45473600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
33	chr10:45471800-45474200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
34	chr10:45472000-45473600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:45472000-45473600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr10:45472000-45473600	Weak transcription	Fetal Lung	lung
37	chr10:45472000-45473600	Transcr. at gene 5' and 3'	Lung	lung
38	chr10:45472000-45473600	Transcr. at gene 5' and 3'	Ovary	ovary
39	chr10:45472000-45473600	Transcr. at gene 5' and 3'	Pancreas	Pancrea
40	chr10:45472000-45474000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:45472000-45474000	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
42	chr10:45472200-45473600	Weak transcription	NH-A	brain
43	chr10:45472200-45473800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr10:45472200-45473800	Transcr. at gene 5' and 3'	HMEC	breast
45	chr10:45472200-45474400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr10:45472400-45473800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:45472600-45473600	Enhancers	Stomach Mucosa	stomach
48	chr10:45472600-45474000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr10:45472600-45474200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:45472600-45474200	Active TSS	Gastric	stomach

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