Variant report

Variant	rs7248168
Chromosome Location	chr19:45685295-45685296
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	POLR2A	chr19:45684307-45685607	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45594755..45598539-chr19:45681810..45685400,4	K562	blood:
2	chr19:45684922..45687661-chr19:45687892..45690396,2	MCF-7	breast:
3	chr19:45684774..45686419-chr19:45697877..45700267,2	MCF-7	breast:
4	chr19:45679504..45683518-chr19:45685241..45688488,5	MCF-7	breast:

Variant related genes	Relation type
TRAPPC6A	TF binding region
ENSG00000007255	Chromatin interaction
ENSG00000225157	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10405306	0.81[CEU][hapmap]
rs10409138	0.84[CEU][hapmap]
rs10421932	0.84[CEU][hapmap]
rs11881409	1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12460041	0.91[GIH][hapmap]
rs17562676	1.00[MKK][hapmap]
rs6509200	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7253652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73564239	0.94[EUR][1000 genomes]
rs73564247	0.94[EUR][1000 genomes]
rs8104024	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8106106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv1794498	chr19:45673701-45691040	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2422482	chr19:45676705-45769805	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	esv1794901	chr19:45681661-45690775	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv833844	chr19:45684309-45887406	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7248168	VN1R2	cis	parietal	SCAN
rs7248168	AP2A1	cis	cerebellum	SCAN
rs7248168	CCDC8	cis	parietal	SCAN
rs7248168	EIF5AP3	cis	lung	GTEx
rs7248168	NANOS2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45682600-45686600	Weak transcription	Fetal Kidney	kidney
2	chr19:45683200-45688200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:45683200-45690400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:45683400-45685600	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr19:45683400-45688200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:45683400-45690600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:45683400-45690800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:45683400-45693200	Weak transcription	Aorta	Aorta
9	chr19:45683600-45685400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:45683600-45686200	Weak transcription	Fetal Lung	lung
11	chr19:45683800-45685400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr19:45683800-45685800	Weak transcription	NH-A	brain
13	chr19:45683800-45686200	Weak transcription	HSMM	muscle
14	chr19:45683800-45686600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:45684000-45685400	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:45684000-45685400	Genic enhancers	Stomach Smooth Muscle	stomach
17	chr19:45684000-45685600	Strong transcription	Fetal Thymus	thymus
18	chr19:45684000-45687800	Weak transcription	Fetal Brain Male	brain
19	chr19:45684000-45688200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:45684000-45690600	Weak transcription	Dnd41	blood
21	chr19:45684000-45695200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:45684200-45685600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:45684200-45685600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:45684400-45685400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr19:45684400-45685600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:45684400-45685800	Strong transcription	Brain Germinal Matrix	brain
27	chr19:45684400-45686200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:45684400-45687800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:45684600-45685400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:45684600-45685400	Genic enhancers	Colon Smooth Muscle	Colon
31	chr19:45684600-45685600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:45684600-45685600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:45684600-45685800	Strong transcription	Fetal Stomach	stomach
34	chr19:45684600-45686000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:45684600-45686000	Weak transcription	HMEC	breast
36	chr19:45684600-45688200	Weak transcription	A549	lung
37	chr19:45684600-45690600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:45684800-45685400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:45684800-45685600	Weak transcription	Brain Substantia Nigra	brain
40	chr19:45684800-45686200	Weak transcription	Left Ventricle	heart
41	chr19:45684800-45686200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:45684800-45686400	Weak transcription	Brain Anterior Caudate	brain
43	chr19:45684800-45686800	Weak transcription	NHLF	lung
44	chr19:45684800-45687200	Weak transcription	NHDF-Ad	bronchial
45	chr19:45684800-45690400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:45684800-45690600	Weak transcription	Stomach Mucosa	stomach
47	chr19:45684800-45690800	Weak transcription	Colonic Mucosa	Colon
48	chr19:45684800-45690800	Weak transcription	Fetal Brain Female	brain
49	chr19:45684800-45691200	Weak transcription	Right Atrium	heart
50	chr19:45684800-45696000	Weak transcription	Fetal Intestine Large	intestine

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