Variant report

Variant	rs9810568
Chromosome Location	chr3:53915276-53915277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53914415-53915418	GM12891	blood:	n/a	n/a
2	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:53915067-53915310	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:53914468-53915393	GM12878	blood:	n/a	n/a
5	USF2	chr3:53915171-53915368	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr3:53915007-53917351	IMR90	lung:	n/a	chr3:53915928-53915938
7	POLR2A	chr3:53914906-53915415	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:53914404-53915445	GM12878	blood:	n/a	n/a
9	MXI1	chr3:53914895-53916494	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:53914925-53916520	GM19099	blood:	n/a	n/a
11	POLR2A	chr3:53914545-53916766	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:53915158-53917310	MCF10A-Er-Src	breast:	n/a	n/a
13	HCFC1	chr3:53915035-53917009	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:53915217-53917615	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:53914423-53917935	GM12891	blood:	n/a	n/a
16	POLR2A	chr3:53914447-53915347	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:53914613-53918608	IMR90	lung:	n/a	n/a
18	POLR2A	chr3:53914533-53917912	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:53914639-53915411	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:53915164-53916311	K562	blood:	n/a	n/a
21	POLR2A	chr3:53914474-53915395	GM12892	blood:	n/a	n/a
22	BRCA1	chr3:53915112-53915517	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:53914664-53917943	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:53914553-53915308	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:53914823-53916702	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr3:53914395-53916554	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:53914433-53916660	GM12892	blood:	n/a	n/a
28	REST	chr3:53914969-53916751	H1-neurons	neurons:	n/a	chr3:53915821-53915834 chr3:53915393-53915406

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53906924..53910795-chr3:53914021..53916121,3	MCF-7	breast:
4	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
5	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
6	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
7	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000113811	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000016391	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]
rs9873491	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53914400-53915400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:53914400-53915400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:53914400-53915400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:53914400-53915400	Flanking Active TSS	HepG2	liver
5	chr3:53914400-53915400	Flanking Active TSS	NH-A	brain
6	chr3:53914600-53915400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:53914600-53915400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:53914600-53915400	Enhancers	Primary B cells from peripheral blood	blood
9	chr3:53914600-53915400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:53914600-53915400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:53914600-53915400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:53914600-53915400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:53914600-53915400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:53914600-53915400	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr3:53914600-53915400	Flanking Active TSS	Colonic Mucosa	Colon
16	chr3:53914600-53915400	Flanking Active TSS	Fetal Brain Female	brain
17	chr3:53914600-53915400	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr3:53914600-53915400	Flanking Active TSS	Fetal Lung	lung
19	chr3:53914600-53915400	Enhancers	Gastric	stomach
20	chr3:53914600-53915400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:53914600-53915400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:53914600-53915400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr3:53914600-53915400	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:53914600-53915400	Flanking Active TSS	Hela-S3	cervix
25	chr3:53914600-53915400	Flanking Active TSS	HMEC	breast
26	chr3:53914600-53915400	Flanking Active TSS	HSMM	muscle
27	chr3:53914600-53915400	Flanking Active TSS	HSMMtube	muscle
28	chr3:53914600-53915400	Flanking Active TSS	HUVEC	blood vessel
29	chr3:53914600-53915400	Flanking Active TSS	Osteobl	bone
30	chr3:53914600-53915600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:53914600-53915600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:53914600-53915600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:53914600-53915600	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr3:53914600-53915600	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr3:53914600-53915600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr3:53914600-53915600	Enhancers	Spleen	Spleen
37	chr3:53914600-53915800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr3:53914800-53915400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:53914800-53915400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
40	chr3:53914800-53915400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:53914800-53915400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr3:53914800-53915400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:53914800-53915400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:53914800-53915400	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr3:53914800-53915400	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr3:53914800-53915400	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr3:53914800-53915400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr3:53914800-53915400	Flanking Active TSS	Fetal Heart	heart
49	chr3:53914800-53915400	Flanking Active TSS	Fetal Kidney	kidney
50	chr3:53914800-53915400	Flanking Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links