Variant report

Variant	rs56378908
Chromosome Location	chr12:48580000-48580001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48578276..48580987-chr12:48583534..48585807,2	K562	blood:
2	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:
3	chr12:48549998..48552316-chr12:48577251..48580205,2	MCF-7	breast:
4	chr12:48579750..48581259-chr12:48592126..48593668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1004746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1004806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506276	0.87[EUR][1000 genomes]
rs10506277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506278	0.87[AMR][1000 genomes]
rs10506280	0.87[AMR][1000 genomes]
rs11830378	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11830864	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11833380	0.89[AMR][1000 genomes]
rs11837419	0.89[AMR][1000 genomes]
rs11837548	0.89[AMR][1000 genomes]
rs11837571	0.89[AMR][1000 genomes]
rs17122802	0.87[EUR][1000 genomes]
rs17122906	0.87[AMR][1000 genomes]
rs17224674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17224828	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17225198	0.89[AMR][1000 genomes]
rs17225261	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225366	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225751	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17226359	0.87[AMR][1000 genomes]
rs17226506	0.87[AMR][1000 genomes]
rs17226723	0.87[AMR][1000 genomes]
rs17607800	0.87[AFR][1000 genomes]
rs17823193	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17823313	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823415	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823565	0.89[AMR][1000 genomes]
rs17824200	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17824705	0.87[AMR][1000 genomes]
rs17824989	0.87[AMR][1000 genomes]
rs17825013	0.87[AMR][1000 genomes]
rs2228501	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3936179	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075914	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41291959	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41291961	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55638557	0.89[AMR][1000 genomes]
rs55654871	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55682541	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55707383	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs55752728	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55763362	0.87[AMR][1000 genomes]
rs55794326	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55854069	0.87[AMR][1000 genomes]
rs55886138	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55890195	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs55894137	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55920439	0.87[AMR][1000 genomes]
rs55945889	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55953382	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56049209	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56084718	0.87[AMR][1000 genomes]
rs56110736	0.87[AMR][1000 genomes]
rs56116946	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56187356	0.96[EUR][1000 genomes]
rs56205628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56271815	0.87[AMR][1000 genomes]
rs56288528	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56383074	0.87[AMR][1000 genomes]
rs56389692	0.87[AMR][1000 genomes]
rs56412095	0.87[AMR][1000 genomes]
rs6580666	0.87[AMR][1000 genomes]
rs7138353	0.89[AMR][1000 genomes]
rs7297558	0.89[AMR][1000 genomes]
rs7301153	0.89[AMR][1000 genomes]
rs7301509	0.89[AMR][1000 genomes]
rs7307383	0.89[AMR][1000 genomes]
rs7307676	0.89[AMR][1000 genomes]
rs7307874	0.89[AMR][1000 genomes]
rs7310715	0.89[AMR][1000 genomes]
rs7310935	0.89[AMR][1000 genomes]
rs73304917	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74089155	0.96[EUR][1000 genomes]
rs74089159	0.85[EUR][1000 genomes]
rs74089163	0.85[EUR][1000 genomes]
rs751315	0.87[AMR][1000 genomes]
rs751316	0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56378908	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:48576800-48580000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:48578000-48580000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr12:48578000-48580400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:48578200-48580400	Enhancers	Esophagus	oesophagus
6	chr12:48578400-48580000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48578400-48580400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48578600-48580000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:48578600-48580200	Active TSS	Brain Angular Gyrus	brain
10	chr12:48578600-48580400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:48578800-48580000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr12:48578800-48580000	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr12:48578800-48580000	Bivalent Enhancer	NHEK	skin
14	chr12:48579000-48580000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr12:48579000-48580400	Bivalent Enhancer	GM12878-XiMat	blood
16	chr12:48579200-48580000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:48579200-48580000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
18	chr12:48579200-48580000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:48579200-48580400	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:48579400-48580000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr12:48579400-48580200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr12:48579400-48580400	Bivalent Enhancer	HSMM	muscle
23	chr12:48579600-48580000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:48579600-48580200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr12:48579600-48580200	Bivalent Enhancer	Hela-S3	cervix
26	chr12:48579600-48580400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:48579600-48580400	Flanking Active TSS	Fetal Brain Female	brain
28	chr12:48579800-48580000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr12:48579800-48580000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr12:48579800-48580200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:48579800-48580200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:48579800-48580400	Enhancers	Brain Anterior Caudate	brain
33	chr12:48579800-48580400	Flanking Active TSS	Fetal Brain Male	brain
34	chr12:48580000-48580200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:48580000-48580200	Bivalent Enhancer	Brain Germinal Matrix	brain
36	chr12:48580000-48580400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:48580000-48580400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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