Variant report

Variant	rs10415452
Chromosome Location	chr19:42382745-42382746
allele	A/G
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	POLR2A	chr19:42380759-42383203	GM12878	blood:	n/a	n/a
2	CTCF	chr19:42382600-42382750	GM12864	blood:	n/a	n/a
3	CTCF	chr19:42382734-42382748	GM10266	blood:	n/a	n/a
4	POLR2A	chr19:42380482-42383380	GM12878	blood:	n/a	n/a
5	CTCF	chr19:42382640-42382790	GM12874	blood:	n/a	chr19:42382743-42382759
6	POLR2A	chr19:42380694-42383289	GM12878	blood:	n/a	n/a
7	CTCF	chr19:42382692-42382780	GM10248	blood:	n/a	chr19:42382743-42382759
8	CTCF	chr19:42382620-42382770	GM12871	blood:	n/a	chr19:42382743-42382759
9	CTCF	chr19:42382680-42382830	GM12864	blood:	n/a	chr19:42382743-42382759
10	POLR2A	chr19:42380562-42384286	GM12892	blood:	n/a	n/a
11	CTCF	chr19:42382662-42382804	HepG2	liver:	n/a	chr19:42382743-42382759
12	CTCF	chr19:42382696-42382796	GM19240	blood:	n/a	chr19:42382743-42382759
13	CTCF	chr19:42382726-42382794	GM19238	blood:	n/a	chr19:42382743-42382759
14	POLR2A	chr19:42382535-42382810	GM12891	blood:	n/a	n/a
15	CTCF	chr19:42382614-42382862	GM12891	blood:	n/a	chr19:42382743-42382759
16	CTCF	chr19:42382720-42382870	GM12873	blood:	n/a	chr19:42382743-42382759
17	POLR2A	chr19:42380748-42382896	GM12891	blood:	n/a	n/a
18	CTCF	chr19:42382732-42382760	H1-hESC	embryonic stem cell:	n/a	chr19:42382743-42382759
19	POLR2A	chr19:42380834-42384163	GM12892	blood:	n/a	n/a
20	CTCF	chr19:42382700-42382850	GM12874	blood:	n/a	chr19:42382743-42382759
21	POLR2A	chr19:42380522-42384559	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:42380674-42382814	Raji	blood:	n/a	n/a
23	CTCF	chr19:42382640-42382790	GM12870	blood:	n/a	chr19:42382743-42382759
24	CTCF	chr19:42382680-42382830	SK-N-SH_RA	brain:	n/a	chr19:42382743-42382759
25	CTCF	chr19:42382669-42382839	GM12892	blood:	n/a	chr19:42382743-42382759
26	CTCF	chr19:42382640-42382790	GM12864	blood:	n/a	chr19:42382743-42382759
27	POLR2A	chr19:42380678-42382921	GM12878	blood:	n/a	n/a
28	CTCF	chr19:42382700-42382850	GM06990	blood:	n/a	chr19:42382743-42382759
29	EBF1	chr19:42380660-42382794	GM12878	blood:	n/a	chr19:42381145-42381155 chr19:42381144-42381155
30	MTA3	chr19:42380510-42383458	GM12878	blood:	n/a	n/a
31	CTCF	chr19:42382636-42382886	GM12878	blood:	n/a	chr19:42382743-42382759
32	POLR2A	chr19:42380742-42382783	GM18505	blood:	n/a	n/a
33	POLR2A	chr19:42380916-42383444	GM12892	blood:	n/a	n/a
34	CTCF	chr19:42382620-42382770	GM12872	blood:	n/a	chr19:42382743-42382759
35	STAT5A	chr19:42380608-42383062	GM12878	blood:	n/a	chr19:42382855-42382867 chr19:42381769-42381781 chr19:42382930-42382942

No.	Distal block	Cell Line	Cell type
1	chr19:42370231..42372294-chr19:42382726..42385087,2	MCF-7	breast:
2	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
3	chr19:42381410..42384062-chr19:42426520..42430266,3	K562	blood:
4	chr19:42382515..42384277-chr19:42396659..42398289,2	MCF-7	breast:
5	chr19:42381223..42383832-chr19:42460147..42462553,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10405900	0.99[ASN][1000 genomes]
rs10417985	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12461099	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12461131	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12972552	0.83[EUR][1000 genomes]
rs12984383	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1366610	0.88[ASN][1000 genomes]
rs1428922	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2075749	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2075750	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2075752	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075754	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3786536	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3786538	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3810153	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58857981	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7250787	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7254214	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257666	0.88[ASN][1000 genomes]
rs7258163	0.84[ASN][1000 genomes]
rs7259596	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259967	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73549152	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8102670	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs873282	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs882520	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs891167	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs930102	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10415452	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42369600-42386400	Weak transcription	Fetal Kidney	kidney
2	chr19:42374600-42386600	Weak transcription	Right Atrium	heart
3	chr19:42375400-42386200	Weak transcription	Hela-S3	cervix
4	chr19:42376000-42386400	Weak transcription	Brain Anterior Caudate	brain
5	chr19:42376000-42386400	Weak transcription	Fetal Lung	lung
6	chr19:42376000-42386600	Weak transcription	HSMMtube	muscle
7	chr19:42376200-42386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:42376200-42386400	Weak transcription	Psoas Muscle	Psoas
9	chr19:42376400-42386400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:42376400-42386400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:42376400-42386400	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:42376400-42386400	Weak transcription	Esophagus	oesophagus
13	chr19:42376400-42386400	Weak transcription	Gastric	stomach
14	chr19:42376400-42386400	Weak transcription	Left Ventricle	heart
15	chr19:42376400-42386400	Weak transcription	HMEC	breast
16	chr19:42376400-42386400	Weak transcription	HUVEC	blood vessel
17	chr19:42376600-42385200	Weak transcription	Right Ventricle	heart
18	chr19:42376600-42386400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:42376600-42386400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:42376600-42386400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:42376600-42386400	Weak transcription	Lung	lung
22	chr19:42376600-42386600	Weak transcription	NHDF-Ad	bronchial
23	chr19:42376800-42386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:42376800-42386400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:42376800-42386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:42377200-42386400	Weak transcription	Brain Angular Gyrus	brain
27	chr19:42377200-42386600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:42377200-42386800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:42377400-42386400	Weak transcription	Pancreas	Pancrea
30	chr19:42377400-42386400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:42377400-42386400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:42377600-42386400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr19:42380200-42386400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:42381000-42382800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:42381000-42382800	Flanking Active TSS	Fetal Thymus	thymus
36	chr19:42381000-42384400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:42381000-42386400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:42381200-42383000	Bivalent Enhancer	Placenta	Placenta
39	chr19:42381200-42383600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:42381400-42383000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:42381600-42382800	Bivalent Enhancer	HepG2	liver
42	chr19:42381600-42384400	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr19:42381600-42385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:42381600-42386200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:42381600-42386400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:42382000-42383000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr19:42382000-42384200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
48	chr19:42382200-42382800	Enhancers	Duodenum Mucosa	Duodenum
49	chr19:42382200-42383000	Active TSS	Spleen	Spleen
50	chr19:42382200-42386200	Enhancers	Primary T cells fromperipheralblood	blood

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