Variant report

Variant	rs4955411
Chromosome Location	chr3:49145304-49145305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49144770-49145438	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49144899-49145327	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:49144907-49145455	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:49144860-49145364	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:49144701-49145471	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49141134-49145325	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:49145237-49145308	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:49145223-49145700	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49145016..49147844-chr3:49150365..49156294,7	K562	blood:
2	chr3:49144937..49146885-chr3:49156947..49158958,2	K562	blood:
3	chr3:49142478..49144078-chr3:49144221..49145872,2	K562	blood:
4	chr3:49130342..49133309-chr3:49142749..49145545,2	K562	blood:
5	chr3:49027258..49030137-chr3:49142521..49145382,2	MCF-7	breast:
6	chr3:49144707..49154191-chr3:49155059..49160099,12	MCF-7	breast:

No data

Variant related genes	Relation type
QARS	TF binding region
ENSG00000198218	Chromatin interaction
ENSG00000223343	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10154992	0.81[ASW][hapmap];0.91[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs11130181	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130183	0.81[ASW][hapmap];0.87[CEU][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs11130186	0.81[ASW][hapmap];0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1134591	0.82[YRI][hapmap]
rs13099075	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3087866	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs3212	0.86[YRI][hapmap]
rs4292260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4364202	0.82[AFR][1000 genomes]
rs4521268	0.82[YRI][hapmap]
rs4955416	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4955417	0.91[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4955421	0.85[YRI][hapmap]
rs4955426	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs4955439	0.87[CEU][hapmap]
rs4955443	0.91[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4974080	0.86[YRI][hapmap]
rs4974081	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4974083	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6446196	0.81[ASW][hapmap];0.86[YRI][hapmap]
rs6446204	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6446205	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6446247	0.85[AMR][1000 genomes]
rs6446256	0.90[CEU][hapmap];0.84[YRI][hapmap]
rs6446257	0.86[CEU][hapmap]
rs6769821	0.87[CEU][hapmap]
rs6772452	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6778080	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs6779394	0.81[ASW][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs6781790	0.82[YRI][hapmap]
rs6787808	0.95[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6803264	0.88[EUR][1000 genomes]
rs6809851	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs7100	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs7373072	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs7373790	0.86[AFR][1000 genomes]
rs7429661	0.87[CEU][hapmap]
rs7430198	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs7432989	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs7434187	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs7617480	0.93[ASW][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7619016	0.91[CEU][hapmap]
rs7621015	0.82[YRI][hapmap]
rs7621347	0.81[EUR][1000 genomes]
rs7626076	0.91[CEU][hapmap]
rs7626445	0.82[YRI][hapmap]
rs7643368	0.82[YRI][hapmap]
rs7653408	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9586	0.87[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs9637481	0.89[YRI][hapmap]
rs9831648	0.87[ASW][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9834003	0.81[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs9840050	0.86[YRI][hapmap]
rs9846123	0.82[YRI][hapmap]
rs9864243	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9865051	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9884022	0.81[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	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs4955411	ZNF589	cis	parietal	SCAN
rs4955411	AMT	cis	Whole Blood	GTEx
rs4955411	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4955411	WDR6	cis	Muscle Skeletal	GTEx
rs4955411	WDR6	cis	cerebellum	SCAN
rs4955411	TLR9	cis	parietal	SCAN
rs4955411	P4HTM	cis	parietal	SCAN
rs4955411	NCKIPSD	cis	Nerve Tibial	GTEx
rs4955411	QRICH1	cis	Nerve Tibial	GTEx
rs4955411	AMT	cis	parietal	SCAN
rs4955411	WDR6	cis	lymphoblastoid	seeQTL
rs4955411	DALRD3	cis	parietal	SCAN
rs4955411	WDR6	cis	Nerve Tibial	GTEx
rs4955411	AMT	cis	Thyroid	GTEx
rs4955411	NICN1	cis	cerebellum	SCAN
rs4955411	AMT	cis	Adipose Subcutaneous	GTEx
rs4955411	AMT	cis	cerebellum	SCAN
rs4955411	WDR6	cis	Heart Left Ventricle	GTEx
rs4955411	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4955411	IQCF1	cis	cerebellum	SCAN
rs4955411	NCKIPSD	cis	parietal	SCAN
rs4955411	NICN1-AS1	cis	Thyroid	GTEx
rs4955411	AMT	cis	Artery Tibial	GTEx
rs4955411	AMT	cis	lymphoblastoid	seeQTL
rs4955411	LZTFL1	cis	cerebellum	SCAN
rs4955411	PHF7	cis	parietal	SCAN
rs4955411	WDR6	cis	lung	GTEx
rs4955411	QRICH1	cis	cerebellum	SCAN
rs4955411	AMT	cis	lung	GTEx
rs4955411	NICN1	cis	parietal	SCAN
rs4955411	NICN1	cis	Thyroid	GTEx
rs4955411	AMT	cis	Artery Aorta	GTEx
rs4955411	AMT	cis	Muscle Skeletal	GTEx
rs4955411	GPX1	cis	parietal	SCAN
rs4955411	DALRD3	cis	cerebellum	SCAN
rs4955411	WDR6	cis	parietal	SCAN
rs4955411	AMT	cis	Nerve Tibial	GTEx
rs4955411	AMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49142800-49145600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:49142800-49145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49142800-49145800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:49142800-49145800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:49142800-49146000	Weak transcription	Ovary	ovary
6	chr3:49142800-49146600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:49142800-49146600	Weak transcription	HSMMtube	muscle
8	chr3:49142800-49146800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:49142800-49146800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:49142800-49146800	Weak transcription	Fetal Kidney	kidney
11	chr3:49142800-49146800	Weak transcription	Stomach Mucosa	stomach
12	chr3:49142800-49146800	Weak transcription	A549	lung
13	chr3:49142800-49147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:49142800-49147000	Weak transcription	Psoas Muscle	Psoas
15	chr3:49142800-49147000	Weak transcription	Small Intestine	intestine
16	chr3:49142800-49147200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:49142800-49147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:49142800-49147200	Weak transcription	K562	blood
19	chr3:49142800-49149000	Weak transcription	NHDF-Ad	bronchial
20	chr3:49142800-49149600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:49142800-49156400	Weak transcription	Right Atrium	heart
22	chr3:49142800-49157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:49142800-49157600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:49143000-49145600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:49143000-49146000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:49143000-49147000	Weak transcription	HSMM	muscle
27	chr3:49143000-49147200	Weak transcription	HMEC	breast
28	chr3:49143000-49153800	Weak transcription	Fetal Brain Male	brain
29	chr3:49143200-49146200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:49143200-49147000	Weak transcription	NH-A	brain
31	chr3:49143400-49145600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:49143400-49145800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:49143400-49146000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:49143400-49146200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:49143400-49146400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:49143400-49147000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:49143400-49147400	Weak transcription	HUVEC	blood vessel
38	chr3:49143600-49145800	Strong transcription	Fetal Intestine Small	intestine
39	chr3:49143600-49146400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:49143600-49146600	Weak transcription	GM12878-XiMat	blood
41	chr3:49143600-49147000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:49143600-49155200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:49143600-49156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:49143600-49156200	Strong transcription	Brain Anterior Caudate	brain
45	chr3:49143600-49156200	Strong transcription	NHLF	lung
46	chr3:49143600-49156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:49143600-49156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:49143600-49156400	Strong transcription	Placenta	Placenta
49	chr3:49143600-49156400	Strong transcription	Fetal Stomach	stomach
50	chr3:49143600-49156400	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links