Variant report

Variant	rs404527
Chromosome Location	chr3:52012000-52012001
allele	C/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	ZNF263	chr3:52011933-52012222	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr3:52011639-52012363	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:52011986-52012033	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254782	TF binding region
ABHD14B	TF binding region
ENSG00000272762	TF binding region
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11916396	1.00[ASN][1000 genomes]
rs11926611	0.81[YRI][hapmap]
rs2015691	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.84[AFR][1000 genomes]
rs323861	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323863	1.00[YRI][hapmap]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323871	0.90[AMR][1000 genomes]
rs323873	0.90[AMR][1000 genomes]
rs323874	0.90[AMR][1000 genomes]
rs323890	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	0.84[YRI][hapmap]
rs323894	0.91[AFR][1000 genomes]
rs323895	0.84[YRI][hapmap]
rs323897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs451154	0.84[AFR][1000 genomes]
rs72964028	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7432986	0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs82854	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52009800-52014400	Weak transcription	Ovary	ovary
2	chr3:52009800-52016400	Weak transcription	Small Intestine	intestine
3	chr3:52010000-52012000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:52010000-52012000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:52010000-52012000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:52010000-52012000	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:52010000-52012200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:52010000-52012200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52010000-52012200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:52010000-52012200	Weak transcription	A549	lung
11	chr3:52010000-52012400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:52010000-52012400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:52010000-52012600	Enhancers	HMEC	breast
14	chr3:52010000-52014200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:52010000-52014400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:52010000-52014400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:52010000-52014600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:52010000-52014800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52010000-52014800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:52010000-52015000	Weak transcription	Hela-S3	cervix
21	chr3:52010000-52015000	Weak transcription	HepG2	liver
22	chr3:52010000-52016400	Weak transcription	Left Ventricle	heart
23	chr3:52010000-52016400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:52010000-52016400	Weak transcription	Psoas Muscle	Psoas
25	chr3:52010000-52016400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:52010000-52016400	Weak transcription	HSMMtube	muscle
27	chr3:52010000-52016400	Weak transcription	NHDF-Ad	bronchial
28	chr3:52010200-52012000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:52010200-52012200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:52010200-52014200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:52010200-52014200	Weak transcription	Fetal Intestine Large	intestine
32	chr3:52010200-52014200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:52010200-52014400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:52010200-52014400	Weak transcription	Fetal Lung	lung
35	chr3:52010200-52014400	Weak transcription	Gastric	stomach
36	chr3:52010200-52014400	Weak transcription	Pancreas	Pancrea
37	chr3:52010200-52014400	Weak transcription	Right Ventricle	heart
38	chr3:52010200-52014400	Weak transcription	Dnd41	blood
39	chr3:52010200-52014600	Weak transcription	Right Atrium	heart
40	chr3:52010200-52014800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52010200-52014800	Weak transcription	Stomach Mucosa	stomach
42	chr3:52010200-52015000	Weak transcription	Colonic Mucosa	Colon
43	chr3:52010200-52015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:52010200-52016000	Weak transcription	Primary B cells from cord blood	blood
45	chr3:52010200-52016200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:52010200-52016200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:52010200-52016200	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:52010200-52016200	Weak transcription	GM12878-XiMat	blood
49	chr3:52010200-52016400	Weak transcription	HSMM	muscle
50	chr3:52010200-52016400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links