Variant report

Variant	rs3087866
Chromosome Location	chr3:49054692-49054693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49052944-49056404	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr3:49054463-49055039	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:49053148-49056378	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49052980-49056417	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:49051503-49056616	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:49052474-49059791	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr3:49053662-49056450	U87	brain:	n/a	n/a
9	POLR2A	chr3:49049681-49055610	GM12891	blood:	n/a	n/a
10	PBX3	chr3:49053536-49056625	SK-N-SH	brain:	n/a	n/a
11	ZNF263	chr3:49054441-49055758	HEK293-T-REx	kidney:	n/a	n/a
12	SIN3AK20	chr3:49054346-49056362	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:49048502-49056486	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49048842-49056486	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:49048845-49056419	GM12891	blood:	n/a	n/a
16	MTA3	chr3:49054570-49056526	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:49052548-49056350	K562	blood:	n/a	n/a
18	POLR2A	chr3:49051566-49056520	GM12878	blood:	n/a	n/a
19	NFATC1	chr3:49054500-49055574	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:49053216-49054717	NB4	blood:	n/a	n/a
21	POLR2A	chr3:49051954-49056421	H1-hESC	embryonic stem cell:	n/a	n/a
22	BCL3	chr3:49053621-49054753	A549	lung:	n/a	n/a
23	POLR2A	chr3:49053617-49056538	U87	brain:	n/a	n/a
24	POLR2A	chr3:49051952-49055393	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:49052566-49055998	A549	lung:	n/a	n/a
26	POLR2A	chr3:49054548-49054897	HCT-116	colon:	n/a	n/a
27	POLR2A	chr3:49050908-49056374	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr3:49052097-49056367	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr3:49052736-49056323	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:49048918-49055399	GM12892	blood:	n/a	n/a
31	POLR2A	chr3:49053331-49056321	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr3:49053819-49054764	GM19193	blood:	n/a	n/a
33	POLR2A	chr3:49048783-49056505	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:49054163-49056367	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:49052798-49054881	SK-N-SH	brain:	n/a	n/a
36	HCFC1	chr3:49054606-49056558	Hela-S3	cervix:	n/a	n/a
37	MTA3	chr3:49053209-49056613	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:49048897-49056290	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:49051541-49056898	K562	blood:	n/a	n/a
40	POLR2A	chr3:49053209-49056861	GM12891	blood:	n/a	n/a
41	MXI1	chr3:49054354-49056631	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:49052889-49056613	HCT-116	colon:	n/a	n/a
43	POU2F2	chr3:49053765-49054803	GM12891	blood:	n/a	n/a
44	POLR2A	chr3:49052846-49056620	K562	blood:	n/a	n/a
45	POLR2A	chr3:49053880-49054871	Hela-S3	cervix:	n/a	n/a
46	PML	chr3:49052717-49056611	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:49052988-49056596	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr3:49053373-49056652	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr3:49052283-49056597	HL-60	blood:	n/a	n/a
50	POLR2A	chr3:49053377-49056256	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49054288..49061452-chr3:49128946..49133927,24	K562	blood:
2	chr3:49052737..49055601-chr3:49169653..49171785,2	MCF-7	breast:
3	chr14:105265057..105267677-chr3:49054198..49056753,2	MCF-7	breast:
4	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
5	chr3:49050440..49054790-chr3:49130798..49133846,4	MCF-7	breast:

No data

Variant related genes	Relation type
DALRD3	TF binding region
NDUFAF3	TF binding region
ENSG00000172037	Chromatin interaction
ENSG00000179627	Chromatin interaction
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11130181	0.86[EUR][1000 genomes]
rs11707968	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12715430	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13084037	1.00[YRI][hapmap]
rs13099075	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4292260	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4955411	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4955416	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4955426	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4955439	0.82[MEX][hapmap]
rs4974081	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974083	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974088	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs62259536	0.81[EUR][1000 genomes]
rs6414614	0.93[EUR][1000 genomes]
rs6446200	0.88[EUR][1000 genomes]
rs6446204	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446247	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446257	0.82[MEX][hapmap]
rs6772452	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787808	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs6798112	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7372883	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7373072	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7429661	0.82[MEX][hapmap]
rs7434187	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621226	0.89[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7621347	0.86[EUR][1000 genomes]
rs7653408	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9284885	0.91[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9810318	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9864243	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9865051	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]

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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	esv3323398	chr3:49053998-49056796	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	esv3339864	chr3:49054573-49057121	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs3087866	AMT	cis	Thyroid	GTEx
rs3087866	WDR6	cis	Heart Left Ventricle	GTEx
rs3087866	QRICH1	cis	cerebellum	SCAN
rs3087866	P4HTM	cis	parietal	SCAN
rs3087866	AMT	cis	Nerve Tibial	GTEx
rs3087866	P4HTM	cis	lung	GTEx
rs3087866	NICN1	cis	cerebellum	SCAN
rs3087866	AMT	cis	Whole Blood	GTEx
rs3087866	PHF7	cis	parietal	SCAN
rs3087866	NCKIPSD	cis	Nerve Tibial	GTEx
rs3087866	NICN1	cis	parietal	SCAN
rs3087866	AMT	cis	lung	GTEx
rs3087866	NCKIPSD	cis	parietal	SCAN
rs3087866	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs3087866	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs3087866	WDR6	cis	Nerve Tibial	GTEx
rs3087866	WDR6	cis	multi-tissue	Pritchard
rs3087866	IQCF1	cis	cerebellum	SCAN
rs3087866	GPX1	cis	parietal	SCAN
rs3087866	DALRD3	cis	cerebellum	SCAN
rs3087866	AMT	cis	Artery Aorta	GTEx
rs3087866	NICN1	cis	Thyroid	GTEx
rs3087866	DALRD3	cis	parietal	SCAN
rs3087866	ARIH2	cis	Thyroid	GTEx
rs3087866	WDR6	cis	cerebellum	SCAN
rs3087866	AMT	cis	Adipose Subcutaneous	GTEx
rs3087866	WDR6	cis	Muscle Skeletal	GTEx
rs3087866	AMT	cis	cerebellum	SCAN
rs3087866	NICN1-AS1	cis	Thyroid	GTEx
rs3087866	WDR6	cis	parietal	SCAN
rs3087866	AMT	cis	Artery Tibial	GTEx
rs3087866	NCKIPSD	cis	multi-tissue	Pritchard
rs3087866	NICN1	cis	multi-tissue	Pritchard
rs3087866	ZNF589	cis	parietal	SCAN
rs3087866	TLR9	cis	parietal	SCAN
rs3087866	AMT	cis	parietal	SCAN
rs3087866	LZTFL1	cis	cerebellum	SCAN
rs3087866	AMT	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49045800-49055000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49046200-49054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:49047600-49054800	Strong transcription	Lung	lung
4	chr3:49048800-49054800	Strong transcription	Brain Cingulate Gyrus	brain
5	chr3:49049200-49054800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:49049200-49054800	Strong transcription	Fetal Lung	lung
7	chr3:49050400-49054800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:49051200-49054800	Weak transcription	Psoas Muscle	Psoas
9	chr3:49051400-49055000	Weak transcription	Right Atrium	heart
10	chr3:49052600-49054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:49053000-49054800	Weak transcription	Small Intestine	intestine
12	chr3:49053000-49054800	Weak transcription	HUVEC	blood vessel
13	chr3:49053400-49056000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:49053600-49054800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:49053600-49054800	Genic enhancers	Pancreas	Pancrea
16	chr3:49053800-49054800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:49053800-49054800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:49053800-49054800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:49053800-49054800	Weak transcription	Fetal Kidney	kidney
20	chr3:49053800-49054800	Weak transcription	Ovary	ovary
21	chr3:49053800-49055000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49053800-49055000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:49053800-49055000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:49053800-49055200	Weak transcription	Aorta	Aorta
25	chr3:49054000-49054800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:49054000-49054800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:49054000-49054800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:49054000-49054800	Weak transcription	Primary B cells from cord blood	blood
29	chr3:49054000-49054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:49054000-49055000	Weak transcription	Gastric	stomach
31	chr3:49054000-49055000	Weak transcription	Left Ventricle	heart
32	chr3:49054000-49055400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:49054200-49054800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:49054200-49054800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:49054200-49054800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:49054200-49054800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:49054200-49054800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:49054200-49054800	Weak transcription	Colonic Mucosa	Colon
39	chr3:49054200-49054800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:49054200-49054800	Genic enhancers	Fetal Intestine Small	intestine
41	chr3:49054200-49054800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:49054200-49054800	Weak transcription	A549	lung
43	chr3:49054200-49055000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:49054200-49055000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr3:49054200-49055000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:49054400-49054800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:49054400-49054800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:49054400-49054800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr3:49054400-49054800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:49054400-49054800	Weak transcription	Adipose Nuclei	Adipose

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