Variant report

Variant	rs12564945
Chromosome Location	chr1:225652605-225652606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:
2	chr1:225597465..225599804-chr1:225650818..225652643,4	K562	blood:
3	chr1:225597626..225599804-chr1:225650818..225652643,2	K562	blood:
4	chr1:225652465..225653214-chr21:44312715..44313565,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000160194	Chromatin interaction
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12564648	0.87[ASN][1000 genomes]
rs12566165	0.87[ASN][1000 genomes]
rs12567909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568642	0.85[ASN][1000 genomes]
rs16845030	0.87[ASN][1000 genomes]
rs16845040	0.85[ASN][1000 genomes]
rs17500644	0.82[ASN][1000 genomes]
rs1771316	0.87[ASN][1000 genomes]
rs2657568	0.85[ASN][1000 genomes]
rs55689260	0.95[ASN][1000 genomes]
rs58088270	0.85[ASN][1000 genomes]
rs58128825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6665838	0.85[ASN][1000 genomes]
rs7544335	0.87[ASN][1000 genomes]
rs7548206	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
3	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
7	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
8	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
13	chr1:225648600-225652800	Weak transcription	Fetal Kidney	kidney
14	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
15	chr1:225649000-225653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:225649200-225652800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
19	chr1:225649400-225653400	Weak transcription	Dnd41	blood
20	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
22	chr1:225650000-225653200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:225650000-225653600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:225650200-225653200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:225650200-225653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:225650200-225653800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:225650200-225654600	Weak transcription	Spleen	Spleen
28	chr1:225650600-225652800	Flanking Active TSS	Hela-S3	cervix
29	chr1:225650600-225653600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:225650800-225653600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:225650800-225653600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:225650800-225653800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:225651000-225653200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:225651000-225653600	Enhancers	HMEC	breast
35	chr1:225651200-225652800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:225651200-225652800	Weak transcription	Fetal Lung	lung
37	chr1:225651200-225653000	Enhancers	Colon Smooth Muscle	Colon
38	chr1:225651200-225653000	Weak transcription	Fetal Brain Female	brain
39	chr1:225651200-225653200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:225651200-225653400	Weak transcription	Right Atrium	heart
41	chr1:225651200-225655200	Weak transcription	Right Ventricle	heart
42	chr1:225651400-225652800	Weak transcription	Adipose Nuclei	Adipose
43	chr1:225651400-225652800	Weak transcription	Left Ventricle	heart
44	chr1:225651400-225653000	Weak transcription	Colonic Mucosa	Colon
45	chr1:225651400-225653600	Weak transcription	Thymus	Thymus
46	chr1:225651400-225654600	Weak transcription	Lung	lung
47	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
48	chr1:225651600-225652800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:225651600-225653200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:225651600-225654400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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