Variant report

Variant	rs57335685
Chromosome Location	chr3:52098458-52098459
allele	C/T
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	chr3:52098416-52098989	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52087881..52090282-chr3:52097638..52100499,3	K562	blood:
2	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf74-1	chr3:52096110-52099128	NONHSAT089896

Variant related genes	Relation type
LINC00696	TF binding region
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.89[EUR][1000 genomes]
rs12386365	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13314125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13319566	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs164638	0.88[EUR][1000 genomes]
rs164639	0.88[EUR][1000 genomes]
rs17051957	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051977	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs171294	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs183029	0.88[EUR][1000 genomes]
rs2304505	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28452586	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28659792	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352146	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs352147	0.88[EUR][1000 genomes]
rs352148	0.89[EUR][1000 genomes]
rs352149	0.89[EUR][1000 genomes]
rs352150	0.88[EUR][1000 genomes]
rs352151	0.89[EUR][1000 genomes]
rs352153	0.91[EUR][1000 genomes]
rs55664415	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55834589	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56281986	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56322622	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57466127	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59890038	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6781635	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72964042	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72964044	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7638246	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs808787	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs876782	0.94[EUR][1000 genomes]
rs893056	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9809254	0.91[EUR][1000 genomes]
rs9809977	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9811707	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9815010	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9816434	0.82[EUR][1000 genomes]
rs9817653	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9830293	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9841469	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843299	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843852	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9846049	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847073	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847092	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9857878	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860982	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9868101	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9882775	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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 lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
3	chr3:52092000-52099200	Weak transcription	Right Atrium	heart
4	chr3:52092000-52102200	Enhancers	HMEC	breast
5	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:52092200-52099200	Weak transcription	Gastric	stomach
7	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
8	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
10	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:52094000-52102000	Enhancers	NHEK	skin
15	chr3:52094200-52098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:52096000-52099200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52096200-52099600	Enhancers	Fetal Muscle Trunk	muscle
19	chr3:52096200-52102000	Enhancers	Fetal Stomach	stomach
20	chr3:52096400-52106400	Weak transcription	Fetal Thymus	thymus
21	chr3:52096600-52099400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:52096600-52099400	Weak transcription	Adipose Nuclei	Adipose
23	chr3:52096600-52100800	Enhancers	Spleen	Spleen
24	chr3:52096800-52104000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:52097000-52098800	Weak transcription	Pancreas	Pancrea
26	chr3:52097000-52099200	Weak transcription	Lung	lung
27	chr3:52097000-52099200	Weak transcription	Right Ventricle	heart
28	chr3:52097000-52099400	Weak transcription	Left Ventricle	heart
29	chr3:52097000-52102000	Weak transcription	Colonic Mucosa	Colon
30	chr3:52097000-52102000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:52097000-52103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:52097000-52105000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:52097000-52105000	Weak transcription	Hela-S3	cervix
34	chr3:52097200-52099200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:52097200-52099200	Weak transcription	HUVEC	blood vessel
36	chr3:52097200-52099400	Weak transcription	Stomach Mucosa	stomach
37	chr3:52097200-52103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:52097200-52104000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:52097400-52099200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:52097400-52099400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52097400-52099400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:52097400-52101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:52097400-52101800	Weak transcription	NHDF-Ad	bronchial
44	chr3:52097400-52104000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52097400-52105400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:52097600-52100000	Bivalent Enhancer	HepG2	liver
48	chr3:52097600-52101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:52097600-52103400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:52097600-52108200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links