Variant report

Variant	rs12895335
Chromosome Location	chr14:24770369-24770370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24702582..24706480-chr14:24770203..24773016,3	K562	blood:
2	chr14:24769506..24771314-chr14:24788379..24791495,3	K562	blood:
3	chr14:24769037..24771886-chr14:24904413..24906460,2	MCF-7	breast:
4	chr14:24701050..24707093-chr14:24765824..24771703,7	K562	blood:
5	chr14:24680927..24686311-chr14:24766466..24771455,6	K562	blood:
6	chr14:24682270..24687913-chr14:24764870..24771791,12	MCF-7	breast:
7	chr14:24655120..24666858-chr14:24765577..24776253,24	MCF-7	breast:
8	chr14:24767930..24771021-chr14:24792565..24795803,5	MCF-7	breast:
9	chr14:24504090..24505966-chr14:24768791..24770568,2	MCF-7	breast:
10	chr14:24767332..24771774-chr14:24910139..24913002,7	MCF-7	breast:
11	chr14:24767097..24775014-chr14:24779936..24787049,14	MCF-7	breast:
12	chr14:24765284..24770509-chr14:24899183..24903551,4	MCF-7	breast:
13	chr14:24740443..24742571-chr14:24769665..24772196,4	K562	blood:
14	chr14:24769087..24772179-chr14:24900488..24904117,5	K562	blood:
15	chr14:24768871..24772362-chr14:24798723..24803416,4	MCF-7	breast:
16	chr14:24768412..24770961-chr14:24898867..24900397,2	K562	blood:
17	chr14:24767708..24770495-chr14:24910481..24913051,4	MCF-7	breast:
18	chr14:24768283..24771076-chr14:24807728..24810560,2	MCF-7	breast:
19	chr14:24766804..24771569-chr14:24898237..24903800,5	MCF-7	breast:
20	chr14:24675521..24677265-chr14:24767958..24770679,2	K562	blood:
21	chr14:24769018..24771644-chr14:24778129..24781269,3	K562	blood:
22	chr14:24768588..24770601-chr14:24787605..24789791,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136305	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000139908	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000272658	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000225766	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000100926	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000100938	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1046587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1051883	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12881984	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884896	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12885593	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12887789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891757	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12892146	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12892419	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12892579	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12895752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12896386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12896469	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295306	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825586	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982889	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4982890	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4982891	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4982892	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4982894	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7146665	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7400863	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7401804	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003991	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941507	0.96[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901499	chr14:24765622-24787588	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
4	nsv901500	chr14:24765622-24793762	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12895335	MYH6	cis	cerebellum	SCAN
rs12895335	DHRS1	cis	Muscle Skeletal	GTEx
rs12895335	ANG	cis	parietal	SCAN
rs12895335	DHRS1	cis	Frontal Cortex	GTEx
rs12895335	FAM158A	cis	parietal	SCAN
rs12895335	DHRS1	cis	parietal	SCAN
rs12895335	RNF31	cis	cerebellum	SCAN
rs12895335	DHRS1	cis	cerebellum	SCAN
rs12895335	TSSK4	cis	parietal	SCAN
rs12895335	DHRS1	cis	multi-tissue	Pritchard
rs12895335	RABGGTA	cis	multi-tissue	Pritchard
rs12895335	CMTM5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24767800-24770400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr14:24768000-24770400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:24768000-24770400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr14:24768200-24770400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr14:24769400-24770400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr14:24769400-24770400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr14:24769400-24770400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr14:24769400-24770400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:24769400-24770400	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr14:24769400-24770600	Flanking Active TSS	Dnd41	blood
11	chr14:24769600-24770400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr14:24769600-24770400	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr14:24769600-24770400	Flanking Active TSS	NHEK	skin
14	chr14:24769800-24770400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr14:24769800-24770400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr14:24769800-24770400	Enhancers	Fetal Heart	heart
17	chr14:24769800-24770400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
18	chr14:24769800-24770600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:24769800-24770800	Enhancers	Stomach Mucosa	stomach
20	chr14:24769800-24771000	Weak transcription	Aorta	Aorta
21	chr14:24770000-24770400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr14:24770000-24770400	Enhancers	Primary B cells from cord blood	blood
23	chr14:24770000-24770400	Enhancers	Primary B cells from peripheral blood	blood
24	chr14:24770000-24770400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:24770000-24770400	Enhancers	Adipose Nuclei	Adipose
26	chr14:24770000-24770400	Enhancers	Fetal Thymus	thymus
27	chr14:24770000-24770400	Enhancers	Small Intestine	intestine
28	chr14:24770000-24770600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr14:24770000-24770600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr14:24770000-24770600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:24770000-24770600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:24770000-24770600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr14:24770000-24770800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:24770000-24770800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:24770000-24770800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr14:24770000-24770800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr14:24770000-24770800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:24770000-24770800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr14:24770000-24771000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:24770000-24771000	Weak transcription	Brain Substantia Nigra	brain
41	chr14:24770000-24771200	Genic enhancers	Fetal Lung	lung
42	chr14:24770000-24771400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:24770000-24773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr14:24770200-24770400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:24770200-24770400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr14:24770200-24770400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:24770200-24770400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:24770200-24770400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr14:24770200-24770400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr14:24770200-24770400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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