Variant report

Variant	rs6781879
Chromosome Location	chr3:111599363-111599364
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	chr3:111599343-111599499	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr3:111599297-111599383	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111599284..111601427-chr3:111601779..111604695,2	K562	blood:

Variant related genes	Relation type
PHLDB2	TF binding region
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10934118	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10934119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934121	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922171	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13064071	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13070728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1500045	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1500046	1.00[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16858901	0.82[YRI][hapmap]
rs2055364	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682322	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682323	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767186	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6786077	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6789911	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6805339	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6805359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649418	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv980070	chr3:111592547-111602240	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6781879	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL
rs6781879	PHLDB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
6	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
8	chr3:111591600-111603200	Weak transcription	Ovary	ovary
9	chr3:111591600-111603600	Weak transcription	HepG2	liver
10	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
12	chr3:111593400-111599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:111593400-111601400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:111593600-111601400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:111593600-111603000	Weak transcription	Lung	lung
17	chr3:111593600-111603200	Weak transcription	Gastric	stomach
18	chr3:111593600-111603400	Weak transcription	HSMM	muscle
19	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:111593800-111601200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:111593800-111602000	Weak transcription	HUVEC	blood vessel
22	chr3:111593800-111602800	Weak transcription	NHLF	lung
23	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
24	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:111593800-111603400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:111594000-111603400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:111594400-111603200	Weak transcription	HMEC	breast
28	chr3:111595200-111601200	Weak transcription	NHEK	skin
29	chr3:111595400-111601200	Weak transcription	Osteobl	bone
30	chr3:111595400-111602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:111598200-111599600	Enhancers	Adipose Nuclei	Adipose
32	chr3:111598200-111600400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:111598400-111612600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:111598600-111600000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:111598800-111599600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr3:111598800-111599600	ZNF genes & repeats	Hela-S3	cervix
37	chr3:111598800-111600200	Enhancers	Right Ventricle	heart
38	chr3:111599000-111599400	ZNF genes & repeats	NH-A	brain
39	chr3:111599000-111600200	Genic enhancers	Left Ventricle	heart
40	chr3:111599000-111600200	ZNF genes & repeats	A549	lung
41	chr3:111599000-111600600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr3:111599200-111599600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:111599200-111600200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:111599200-111600200	ZNF genes & repeats	Liver	Liver
45	chr3:111599200-111600400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:111599200-111600400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:111599200-111600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:111599200-111600400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr3:111599200-111603400	Weak transcription	Right Atrium	heart

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