Variant report

Variant	rs9877046
Chromosome Location	chr3:50352458-50352459
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50351736-50353412	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:50351725-50353273	HUVEC	blood vessel:	n/a	n/a
3	MYC	chr3:50352432-50352590	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:50352145-50353015	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:50351308-50353418	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:50352447-50353236	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:50352350-50352513	K562	blood:	n/a	n/a
8	POLR2A	chr3:50351957-50353077	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr3:50351508-50353392	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:50352115-50352952	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:50352456-50352536	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:50352448-50352635	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
2	chr3:50327926..50342388-chr3:50350886..50359960,36	MCF-7	breast:
3	chr3:50296581..50299334-chr3:50352263..50355118,3	MCF-7	breast:
4	chr3:50300460..50314689-chr3:50349154..50363682,34	MCF-7	breast:
5	chr3:50351771..50356225-chr3:50370784..50376711,6	MCF-7	breast:
6	chr3:50329346..50330939-chr3:50352382..50354518,2	K562	blood:

No data

Variant related genes	Relation type
HYAL1	TF binding region
ENSG00000186792	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000114378	Chromatin interaction
ENSG00000068028	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1076872	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11716295	1.00[LWK][hapmap]
rs11917680	0.94[CHD][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs12637870	0.94[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap]
rs2236989	0.94[CHD][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2282755	0.81[CEU][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs41499647	0.94[CHD][hapmap]
rs4547694	0.82[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap]
rs709210	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs762707	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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
9	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
10	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
11	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	83 gene(s)	inside rSNPs	diseases
18	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
19	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
20	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
21	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9877046	PTH1R	cis	parietal	SCAN
rs9877046	PER3	trans	lymphoblastoid	seeQTL
rs9877046	HYAL3	cis	Esophagus Muscularis	GTEx
rs9877046	HYAL3	cis	multi-tissue	Pritchard
rs9877046	RNF123	cis	parietal	SCAN
rs9877046	HYAL3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50337800-50353800	Weak transcription	HSMMtube	muscle
2	chr3:50338200-50352800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:50338200-50353800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:50338200-50353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:50338200-50353800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:50338200-50356000	Weak transcription	Primary T cells from cord blood	blood
7	chr3:50338400-50352800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:50338600-50355600	Weak transcription	Fetal Brain Male	brain
9	chr3:50338600-50355800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:50338800-50352600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:50338800-50353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:50338800-50354000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:50339200-50353000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:50340800-50354200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:50340800-50355400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:50341000-50352800	Weak transcription	Fetal Lung	lung
17	chr3:50341000-50353400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:50341000-50353800	Weak transcription	Colonic Mucosa	Colon
19	chr3:50341000-50353800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:50341000-50353800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:50341000-50353800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:50341400-50353800	Weak transcription	Ovary	ovary
23	chr3:50341400-50354000	Weak transcription	Right Atrium	heart
24	chr3:50341400-50354200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:50341400-50355600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:50341400-50357600	Weak transcription	NHDF-Ad	bronchial
27	chr3:50342600-50357000	Weak transcription	HSMM	muscle
28	chr3:50346200-50352600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:50347200-50354200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:50347400-50352600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:50347400-50353800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:50347400-50353800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:50347600-50352800	Weak transcription	HMEC	breast
34	chr3:50347600-50353800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:50347600-50353800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:50347600-50353800	Weak transcription	A549	lung
37	chr3:50347800-50352800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:50347800-50353800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:50347800-50353800	Weak transcription	Dnd41	blood
40	chr3:50347800-50353800	Weak transcription	HepG2	liver
41	chr3:50348000-50353600	Weak transcription	NHEK	skin
42	chr3:50348000-50353800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:50348000-50354400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:50349400-50354400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:50349600-50354000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:50349800-50353800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:50350000-50352800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:50350400-50353600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:50350400-50355400	Weak transcription	Osteobl	bone
50	chr3:50350600-50354600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links