Variant report

Variant	rs55834589
Chromosome Location	chr3:52081724-52081725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52063546..52065859-chr3:52080631..52082453,2	MCF-7	breast:
2	chr3:52081717..52084424-chr3:52095750..52098933,3	K562	blood:
3	chr3:52077892..52079847-chr3:52080984..52082911,3	MCF-7	breast:
4	chr3:52071945..52074721-chr3:52081198..52083628,2	K562	blood:
5	chr3:52048463..52050147-chr3:52081246..52082916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256097	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs123681	0.86[EUR][1000 genomes]
rs12386365	0.87[EUR][1000 genomes]
rs13314125	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13319566	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs164638	0.85[EUR][1000 genomes]
rs164639	0.85[EUR][1000 genomes]
rs17051957	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17051977	0.88[EUR][1000 genomes]
rs171294	0.86[EUR][1000 genomes]
rs183029	0.85[EUR][1000 genomes]
rs2304505	0.88[EUR][1000 genomes]
rs28452586	0.88[EUR][1000 genomes]
rs28659792	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs352146	0.85[EUR][1000 genomes]
rs352147	0.85[EUR][1000 genomes]
rs352148	0.86[EUR][1000 genomes]
rs352149	0.86[EUR][1000 genomes]
rs352150	0.85[EUR][1000 genomes]
rs352151	0.86[EUR][1000 genomes]
rs352153	0.88[EUR][1000 genomes]
rs55664415	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56281986	0.86[EUR][1000 genomes]
rs56322622	0.88[EUR][1000 genomes]
rs57335685	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57466127	0.88[EUR][1000 genomes]
rs59890038	0.91[EUR][1000 genomes]
rs6781635	0.88[EUR][1000 genomes]
rs72964042	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72964044	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638246	0.81[EUR][1000 genomes]
rs808787	0.86[EUR][1000 genomes]
rs876782	0.91[EUR][1000 genomes]
rs893056	0.91[EUR][1000 genomes]
rs9809254	0.88[EUR][1000 genomes]
rs9809977	0.91[EUR][1000 genomes]
rs9811707	0.88[EUR][1000 genomes]
rs9815010	0.88[EUR][1000 genomes]
rs9817653	0.91[EUR][1000 genomes]
rs9830293	0.88[EUR][1000 genomes]
rs9841469	0.91[EUR][1000 genomes]
rs9843299	0.91[EUR][1000 genomes]
rs9843852	0.88[EUR][1000 genomes]
rs9846049	0.91[EUR][1000 genomes]
rs9847073	0.91[EUR][1000 genomes]
rs9847092	0.82[EUR][1000 genomes]
rs9857878	0.91[EUR][1000 genomes]
rs9860982	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9868101	0.91[EUR][1000 genomes]
rs9882775	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv1792042	chr3:52070955-52091254	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1793040	chr3:52070955-52091254	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797975	chr3:52070955-52091254	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1798814	chr3:52070955-52091254	Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	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
16	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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52074000-52083200	Weak transcription	Pancreas	Pancrea
2	chr3:52074400-52083200	Weak transcription	Liver	Liver
3	chr3:52076000-52086400	Weak transcription	Fetal Brain Male	brain
4	chr3:52077200-52081800	Enhancers	Brain Substantia Nigra	brain
5	chr3:52077400-52081800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr3:52077400-52082400	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:52077400-52082400	Enhancers	Esophagus	oesophagus
8	chr3:52077600-52081800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:52077600-52083400	Enhancers	Brain Angular Gyrus	brain
10	chr3:52077800-52082400	Weak transcription	Fetal Intestine Large	intestine
11	chr3:52077800-52082400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:52077800-52083400	Weak transcription	Primary B cells from cord blood	blood
13	chr3:52078000-52081800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:52078000-52083200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52078000-52083400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:52078000-52084000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:52078200-52083800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:52078200-52084200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:52078400-52081800	Enhancers	Right Ventricle	heart
20	chr3:52078400-52082200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:52078600-52084200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:52078800-52083200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52078800-52083200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:52079200-52081800	Enhancers	Lung	lung
25	chr3:52079200-52082000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:52079200-52082000	Weak transcription	Primary T cells from cord blood	blood
27	chr3:52079200-52082200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:52079200-52082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:52079200-52082400	Enhancers	Fetal Muscle Leg	muscle
30	chr3:52079400-52082000	Enhancers	Left Ventricle	heart
31	chr3:52079400-52082200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:52079400-52082200	Enhancers	Right Atrium	heart
33	chr3:52079400-52082400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr3:52079400-52082400	Enhancers	Spleen	Spleen
35	chr3:52079400-52082600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:52079400-52082800	Enhancers	HUVEC	blood vessel
37	chr3:52079600-52081800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:52079600-52082000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:52079600-52082200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:52079600-52083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:52079800-52082200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:52079800-52082400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:52079800-52083400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:52079800-52083600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:52079800-52084000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52079800-52085000	Weak transcription	K562	blood
47	chr3:52080000-52082000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52080000-52082000	Flanking Active TSS	Hela-S3	cervix
49	chr3:52080000-52082200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:52080000-52082600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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