Variant report

Variant	rs7248200
Chromosome Location	chr19:19744452-19744453
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:6)
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	CEBPB	chr19:19744367-19744454	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:19744381-19744959	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19650704..19652746-chr19:19743120..19746086,2	K562	blood:
2	chr19:19736608..19739884-chr19:19741504..19746062,6	K562	blood:
3	chr19:19742582..19744978-chr19:19752579..19757681,5	MCF-7	breast:
4	chr19:19739295..19742489-chr19:19743481..19745918,5	MCF-7	breast:
5	chr19:19743070..19745753-chr19:20069128..20070689,2	MCF-7	breast:
6	chr19:19743338..19745792-chr19:19752799..19756349,4	K562	blood:

No data

Variant related genes	Relation type
LPAR2	TF binding region
ENSG00000089639	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000160161	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10407283	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416924	0.81[JPT][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap]
rs10417097	0.81[JPT][hapmap]
rs1054685	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs12609436	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511040	0.86[YRI][hapmap]
rs6511046	0.86[LWK][hapmap];0.87[MEX][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs7248885	0.81[JPT][hapmap]
rs873870	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs880090	0.96[YRI][hapmap];0.82[AFR][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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7248200	CYP4F8	cis	cerebellum	SCAN
rs7248200	NR2C2AP	cis	parietal	SCAN
rs7248200	OCEL1	cis	parietal	SCAN
rs7248200	NRSN1	trans	parietal	SCAN
rs7248200	OR10H4	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19735000-19753200	Weak transcription	K562	blood
2	chr19:19738600-19753000	Weak transcription	Fetal Brain Male	brain
3	chr19:19738800-19752800	Weak transcription	Stomach Mucosa	stomach
4	chr19:19739000-19745000	Weak transcription	HSMM	muscle
5	chr19:19739800-19744600	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:19739800-19744800	Weak transcription	Esophagus	oesophagus
7	chr19:19739800-19744800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:19739800-19745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:19739800-19745200	Weak transcription	Right Ventricle	heart
10	chr19:19739800-19745600	Weak transcription	Ovary	ovary
11	chr19:19739800-19752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:19739800-19753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
14	chr19:19739800-19753400	Weak transcription	HMEC	breast
15	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
16	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
17	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
18	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
19	chr19:19740000-19744600	Weak transcription	Gastric	stomach
20	chr19:19740000-19744800	Weak transcription	Colonic Mucosa	Colon
21	chr19:19740000-19744800	Weak transcription	Pancreas	Pancrea
22	chr19:19740000-19745000	Weak transcription	Fetal Lung	lung
23	chr19:19740000-19745000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:19740000-19745000	Weak transcription	A549	lung
25	chr19:19740000-19745200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:19740000-19745200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:19740000-19746000	Weak transcription	NH-A	brain
28	chr19:19740000-19753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19740000-19753400	Weak transcription	Brain Anterior Caudate	brain
30	chr19:19740000-19753600	Weak transcription	Fetal Kidney	kidney
31	chr19:19740200-19745800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:19740200-19745800	Strong transcription	GM12878-XiMat	blood
33	chr19:19740200-19746000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:19740200-19747600	Strong transcription	Thymus	Thymus
35	chr19:19740200-19748800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:19740200-19751200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:19740200-19751400	Strong transcription	Lung	lung
38	chr19:19740200-19751400	Strong transcription	Dnd41	blood
39	chr19:19740200-19753000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:19740400-19744800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:19740400-19745600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:19740400-19745800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:19740400-19747600	Strong transcription	Spleen	Spleen
44	chr19:19740400-19748200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:19740400-19750000	Strong transcription	Primary B cells from cord blood	blood
46	chr19:19740400-19751400	Strong transcription	Fetal Thymus	thymus
47	chr19:19740400-19751600	Strong transcription	Brain Germinal Matrix	brain
48	chr19:19740400-19752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19740600-19745000	Weak transcription	Hela-S3	cervix
50	chr19:19740600-19745600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links