Variant report

Variant	rs17823313
Chromosome Location	chr12:48598510-48598511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48597340..48600068-chr12:48604806..48607585,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1004746	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1004806	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10506276	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506277	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10506279	0.89[AMR][1000 genomes]
rs11830378	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830617	1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833380	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835509	1.00[ASN][1000 genomes]
rs11837419	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837571	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122802	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17224674	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17224828	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225198	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225261	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17225366	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17225751	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823193	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823415	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823565	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824200	0.89[AMR][1000 genomes]
rs34093317	1.00[ASN][1000 genomes]
rs55638557	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55794326	0.89[AMR][1000 genomes]
rs56048326	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56116946	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56205628	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56378908	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7138353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297558	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301153	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301509	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307874	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310715	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310935	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73304917	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74089125	1.00[ASN][1000 genomes]
rs74089159	0.89[EUR][1000 genomes]
rs74089163	0.89[EUR][1000 genomes]
rs9630296	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv518743	chr12:48597507-48600520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17823313	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
4	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:48594200-48598600	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:48594200-48598800	Weak transcription	Fetal Heart	heart
7	chr12:48594800-48599000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:48595200-48598600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:48595200-48598600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:48595200-48598800	Weak transcription	Fetal Lung	lung
11	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
12	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
13	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:48596600-48603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:48596800-48598600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:48597000-48598600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:48597000-48606600	Weak transcription	Left Ventricle	heart
20	chr12:48597000-48606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:48597200-48598600	Weak transcription	Gastric	stomach
22	chr12:48597200-48598600	Weak transcription	Ovary	ovary
23	chr12:48597800-48599200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
24	chr12:48598000-48599600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr12:48598200-48599200	ZNF genes & repeats	Brain Anterior Caudate	brain
26	chr12:48598400-48599000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:48598400-48599000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
28	chr12:48598400-48599200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr12:48598400-48599200	ZNF genes & repeats	Adipose Nuclei	Adipose
30	chr12:48598400-48599200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
31	chr12:48598400-48599400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr12:48598400-48599400	Strong transcription	Brain Cingulate Gyrus	brain
33	chr12:48598400-48599400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:48598400-48599400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:48598400-48599600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr12:48598400-48600200	Weak transcription	Brain Hippocampus Middle	brain

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