Variant report

Variant	rs9873491
Chromosome Location	chr3:53918066-53918067
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	chr3:53915666-53918109	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:53914613-53918608	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:53917607-53918144	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:53915500-53918115	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:53916006-53918522	A549	lung:	n/a	n/a
6	POLR2A	chr3:53915599-53918118	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
2	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
3	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
4	chr3:53906811..53909807-chr3:53917602..53920226,2	MCF-7	breast:

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000222888	TF binding region
ENSG00000113811	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs58284360	0.90[AFR][1000 genomes]
rs58746828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6774651	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798958	0.90[AFR][1000 genomes]
rs72972853	1.00[AMR][1000 genomes]
rs72972854	1.00[AMR][1000 genomes]
rs9810568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53916200-53919400	Weak transcription	Spleen	Spleen
2	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53916600-53918200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:53916600-53918400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:53916600-53918400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:53916600-53918400	Weak transcription	Ovary	ovary
8	chr3:53916600-53918400	Weak transcription	HMEC	breast
9	chr3:53916600-53918600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:53916600-53918600	Weak transcription	Lung	lung
11	chr3:53916600-53918600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:53916600-53918600	Weak transcription	Right Ventricle	heart
13	chr3:53916600-53918800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:53916600-53918800	Weak transcription	Placenta	Placenta
15	chr3:53916600-53919200	Weak transcription	Colonic Mucosa	Colon
16	chr3:53916600-53919400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:53916600-53921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:53916600-53921800	Strong transcription	HSMM	muscle
19	chr3:53916600-53922000	Weak transcription	K562	blood
20	chr3:53916600-53923400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:53916600-53924000	Weak transcription	Psoas Muscle	Psoas
22	chr3:53916600-53924000	Weak transcription	A549	lung
23	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
24	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
27	chr3:53916800-53918200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:53916800-53918200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:53916800-53918400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:53916800-53918400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:53916800-53918400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:53916800-53918400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:53916800-53918400	Weak transcription	Adipose Nuclei	Adipose
34	chr3:53916800-53918400	Weak transcription	Brain Anterior Caudate	brain
35	chr3:53916800-53918600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:53916800-53918600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:53916800-53918600	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:53916800-53918600	Weak transcription	Fetal Lung	lung
39	chr3:53916800-53918600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:53916800-53918600	Weak transcription	NHDF-Ad	bronchial
41	chr3:53916800-53918800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:53916800-53918800	Weak transcription	Small Intestine	intestine
43	chr3:53916800-53918800	Weak transcription	Hela-S3	cervix
44	chr3:53916800-53919400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:53916800-53919400	Weak transcription	HSMMtube	muscle
46	chr3:53916800-53919400	Weak transcription	NHEK	skin
47	chr3:53916800-53920000	Weak transcription	Primary T cells from cord blood	blood
48	chr3:53916800-53920800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:53916800-53921000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:53916800-53921200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links