Variant report

Variant	rs9858497
Chromosome Location	chr3:51419085-51419086
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	chr3:51418504-51419446	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr3:51418669-51421142	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:51418535-51424565	K562	blood:	n/a	n/a
4	POLR2A	chr3:51418534-51420289	Raji	blood:	n/a	n/a
5	POLR2A	chr3:51418859-51419298	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51416005..51420526-chr3:51420969..51426466,5	MCF-7	breast:

Variant related genes	Relation type
MANF	TF binding region
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12330534	1.00[AMR][1000 genomes]
rs13314120	1.00[AMR][1000 genomes]
rs13321674	1.00[AMR][1000 genomes]
rs13433729	0.85[AMR][1000 genomes]
rs17051799	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051832	1.00[AMR][1000 genomes]
rs17081501	1.00[AMR][1000 genomes]
rs28421789	0.85[AMR][1000 genomes]
rs28452990	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28457212	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2883900	0.85[AMR][1000 genomes]
rs4549265	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58807639	1.00[ASN][1000 genomes]
rs59525691	1.00[AMR][1000 genomes]
rs60823123	1.00[AMR][1000 genomes]
rs72951441	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951452	1.00[AMR][1000 genomes]
rs72951472	1.00[AMR][1000 genomes]
rs72951485	1.00[AMR][1000 genomes]
rs72951486	1.00[AMR][1000 genomes]
rs72953413	0.85[AMR][1000 genomes]
rs72953417	1.00[AMR][1000 genomes]
rs72953423	0.85[AMR][1000 genomes]
rs753452	1.00[ASN][1000 genomes]
rs904144	0.85[AMR][1000 genomes]
rs9311470	0.85[AMR][1000 genomes]
rs9808940	0.85[AMR][1000 genomes]
rs9809757	1.00[AMR][1000 genomes]
rs9812008	1.00[AMR][1000 genomes]
rs9815684	1.00[AMR][1000 genomes]
rs9816075	1.00[AMR][1000 genomes]
rs9824779	1.00[AMR][1000 genomes]
rs9826664	0.85[AMR][1000 genomes]
rs9827665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827917	1.00[AMR][1000 genomes]
rs9838294	1.00[AMR][1000 genomes]
rs9838942	1.00[AMR][1000 genomes]
rs9838994	1.00[AMR][1000 genomes]
rs9839516	0.85[AMR][1000 genomes]
rs9839608	1.00[AMR][1000 genomes]
rs9840331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	1.00[AMR][1000 genomes]
rs9855809	0.85[AMR][1000 genomes]
rs9857893	1.00[AMR][1000 genomes]
rs9864213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866513	1.00[AMR][1000 genomes]
rs9866604	0.85[AMR][1000 genomes]
rs9870147	1.00[AMR][1000 genomes]
rs9880909	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9881402	1.00[AMR][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	1.00[AMR][1000 genomes]
rs9990341	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
3	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
4	chr3:51406000-51420200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:51406000-51420400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:51406000-51420400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:51406000-51420600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:51406000-51420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:51406000-51420800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:51406000-51421400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:51406400-51420600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:51406400-51421600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:51410000-51421400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:51410400-51420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:51410600-51419200	Weak transcription	Fetal Stomach	stomach
16	chr3:51411000-51420000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr3:51411000-51420000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr3:51411200-51420000	Strong transcription	Fetal Brain Female	brain
19	chr3:51412400-51420600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:51413800-51419800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:51414400-51420600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:51414600-51419600	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:51414800-51421400	Weak transcription	HSMMtube	muscle
24	chr3:51415200-51421200	Weak transcription	Brain Angular Gyrus	brain
25	chr3:51415400-51420800	Weak transcription	Brain Anterior Caudate	brain
26	chr3:51415600-51420600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:51416600-51419600	Strong transcription	Brain Hippocampus Middle	brain
28	chr3:51416600-51420800	Weak transcription	NHEK	skin
29	chr3:51416800-51419600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:51417000-51419400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:51417000-51420400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:51417000-51420600	Weak transcription	GM12878-XiMat	blood
33	chr3:51417200-51420600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:51417200-51421000	Weak transcription	HSMM	muscle
35	chr3:51417200-51421400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:51417400-51420600	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:51417400-51420800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:51417400-51420800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:51417600-51420600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:51417600-51420800	Weak transcription	Primary T cells from cord blood	blood
41	chr3:51417600-51421400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:51417600-51421600	Weak transcription	Spleen	Spleen
43	chr3:51417800-51420400	Weak transcription	Brain Germinal Matrix	brain
44	chr3:51417800-51421000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:51418000-51420800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr3:51418000-51420800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:51418000-51421200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:51418000-51421400	Weak transcription	Thymus	Thymus
49	chr3:51418400-51420600	Weak transcription	Dnd41	blood
50	chr3:51418400-51420800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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