Variant report

Variant	rs7248167
Chromosome Location	chr19:43960114-43960115
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:43959936..43961560-chr19:44019524..44021697,2	MCF-7	breast:
2	chr19:43959047..43960666-chr19:44006896..44009255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12973764	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap]
rs12980646	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap]
rs12981023	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2102954	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs304731	0.81[CEU][hapmap]
rs34352751	0.80[ASN][1000 genomes]
rs35765283	0.90[ASN][1000 genomes]
rs4802183	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs4802185	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs7253856	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs8111567	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv520852	chr19:43885085-43960114	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv579850	chr19:43885085-43960114	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7248167	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs7248167	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs7248167	APOE	cis	parietal	SCAN
rs7248167	BLOC1S3	cis	parietal	SCAN
rs7248167	KCNJ14	cis	cerebellum	SCAN
rs7248167	ETHE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43951200-43964800	Weak transcription	Esophagus	oesophagus
2	chr19:43957000-43967000	Weak transcription	Spleen	Spleen
3	chr19:43958200-43960600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr19:43959000-43960200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:43959400-43960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr19:43959400-43960200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:43959400-43960200	Enhancers	Placenta	Placenta
8	chr19:43959600-43960200	Enhancers	Duodenum Mucosa	Duodenum
9	chr19:43959600-43960200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr19:43959600-43960200	Enhancers	Stomach Smooth Muscle	stomach
11	chr19:43959600-43960200	Enhancers	HMEC	breast
12	chr19:43959600-43960200	Flanking Active TSS	NHEK	skin
13	chr19:43959600-43960400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:43959600-43960400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:43959600-43960400	Enhancers	Liver	Liver
16	chr19:43959600-43960400	Enhancers	HepG2	liver
17	chr19:43959600-43960400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:43959600-43960600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:43959800-43960200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:43959800-43960200	Enhancers	Colonic Mucosa	Colon
21	chr19:43959800-43960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:43959800-43960400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:43959800-43964800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:43959800-43967000	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:43960000-43960200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr19:43960000-43960200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:43960000-43960200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr19:43960000-43960200	Enhancers	Small Intestine	intestine
29	chr19:43960000-43960200	Enhancers	K562	blood
30	chr19:43960000-43960400	Enhancers	Primary B cells from peripheral blood	blood
31	chr19:43960000-43960400	Enhancers	Primary hematopoietic stem cells	blood

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