Variant report

Variant	rs3736309
Chromosome Location	chr12:50358054-50358055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50353765..50356841-chr12:50356981..50360242,4	MCF-7	breast:
2	chr12:50356903..50358406-chr12:50425731..50427880,2	MCF-7	breast:
3	chr12:50352910..50356046-chr12:50357826..50360762,4	K562	blood:

Variant related genes	Relation type
ENSG00000161798	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000257588	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11169270	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899073	chr12:50335628-50360461	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv899074	chr12:50344976-50360461	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1828759	chr12:50349765-50366300	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv1827130	chr12:50349765-50379667	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv523899	chr12:50354437-50366300	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv558838	chr12:50355329-50358054	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv558839	chr12:50355381-50358468	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3736309	ADCY6	cis	cerebellum	SCAN
rs3736309	DDX23	cis	cerebellum	SCAN
rs3736309	SNORA2B	cis	parietal	SCAN
rs3736309	NCKAP5L	cis	parietal	SCAN
rs3736309	KRT7	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50353600-50358400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:50355400-50358200	Enhancers	Pancreas	Pancrea
3	chr12:50355400-50361200	Weak transcription	Lung	lung
4	chr12:50356000-50361000	Weak transcription	Ovary	ovary
5	chr12:50356800-50359000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:50356800-50361000	Weak transcription	Brain Anterior Caudate	brain
7	chr12:50357000-50360600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:50357000-50360600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:50357000-50360800	Weak transcription	Fetal Brain Female	brain
10	chr12:50357200-50358400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:50357200-50360800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:50357400-50360400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:50357400-50360400	Enhancers	Hela-S3	cervix
14	chr12:50357400-50360600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:50357400-50360600	Weak transcription	Fetal Brain Male	brain
16	chr12:50357400-50360600	Weak transcription	Spleen	Spleen
17	chr12:50357400-50360800	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:50357400-50361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:50357400-50361000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:50357400-50361000	Weak transcription	Right Ventricle	heart
21	chr12:50357400-50361000	Weak transcription	HMEC	breast
22	chr12:50357400-50361000	Weak transcription	HSMMtube	muscle
23	chr12:50357400-50361000	Weak transcription	HUVEC	blood vessel
24	chr12:50357600-50358200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:50357600-50360000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:50357600-50361000	Weak transcription	Left Ventricle	heart
27	chr12:50357800-50359800	Weak transcription	Brain Germinal Matrix	brain
28	chr12:50357800-50360600	Weak transcription	Esophagus	oesophagus
29	chr12:50357800-50360600	Weak transcription	A549	lung
30	chr12:50357800-50360800	Weak transcription	Liver	Liver
31	chr12:50357800-50361000	Weak transcription	Right Atrium	heart
32	chr12:50357800-50366400	Weak transcription	Gastric	stomach
33	chr12:50358000-50359000	Bivalent Enhancer	HepG2	liver
34	chr12:50358000-50361000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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