Variant report

Variant	rs2738809
Chromosome Location	chr16:75516739-75516740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75496707..75498493-chr16:75515933..75518742,2	MCF-7	breast:
2	chr16:75506694..75509130-chr16:75514124..75517050,2	MCF-7	breast:
3	chr16:75515909..75518493-chr16:75681322..75683050,2	MCF-7	breast:
4	chr16:75516147..75519691-chr16:75524437..75526173,3	MCF-7	breast:
5	chr16:75514359..75521343-chr16:75549270..75552665,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065427	Chromatin interaction
ENSG00000261717	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000262583	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs100912	0.95[ASN][1000 genomes]
rs1030261	0.85[ASN][1000 genomes]
rs1030262	0.86[ASN][1000 genomes]
rs10871312	0.85[ASN][1000 genomes]
rs10871313	0.90[ASN][1000 genomes]
rs11641249	0.91[ASN][1000 genomes]
rs11641430	0.88[ASN][1000 genomes]
rs11643207	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11644306	0.86[ASN][1000 genomes]
rs11649638	0.85[ASN][1000 genomes]
rs12051137	0.86[ASN][1000 genomes]
rs12446877	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12918797	0.88[ASN][1000 genomes]
rs12924333	0.83[ASN][1000 genomes]
rs12927562	0.85[ASN][1000 genomes]
rs12928036	0.85[ASN][1000 genomes]
rs12933281	0.85[ASN][1000 genomes]
rs1424013	0.88[ASN][1000 genomes]
rs17696831	0.88[ASN][1000 genomes]
rs1834013	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1834014	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2161684	0.83[ASN][1000 genomes]
rs247454	0.97[ASN][1000 genomes]
rs2738812	0.86[ASN][1000 genomes]
rs2738813	0.86[ASN][1000 genomes]
rs2738814	0.89[ASN][1000 genomes]
rs28558946	0.85[ASN][1000 genomes]
rs28655617	0.84[ASN][1000 genomes]
rs3115960	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34539062	0.88[ASN][1000 genomes]
rs34918083	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34996006	0.82[ASN][1000 genomes]
rs35214308	0.82[ASN][1000 genomes]
rs35683383	0.83[ASN][1000 genomes]
rs37592	0.88[ASN][1000 genomes]
rs37593	0.88[ASN][1000 genomes]
rs37594	0.88[ASN][1000 genomes]
rs37595	0.88[ASN][1000 genomes]
rs37597	0.81[ASN][1000 genomes]
rs37606	0.91[ASN][1000 genomes]
rs40446	0.88[ASN][1000 genomes]
rs4887829	0.85[ASN][1000 genomes]
rs4888425	0.82[ASN][1000 genomes]
rs4888426	0.82[ASN][1000 genomes]
rs4888427	0.83[ASN][1000 genomes]
rs4888430	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888431	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888432	0.87[ASN][1000 genomes]
rs56116092	0.89[ASN][1000 genomes]
rs59155720	0.83[ASN][1000 genomes]
rs59347518	0.82[ASN][1000 genomes]
rs59465235	0.85[ASN][1000 genomes]
rs62060550	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62060551	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564261	0.88[ASN][1000 genomes]
rs7193828	0.87[ASN][1000 genomes]
rs7194035	0.87[ASN][1000 genomes]
rs7195161	0.88[ASN][1000 genomes]
rs7198873	0.81[ASN][1000 genomes]
rs7199062	0.82[ASN][1000 genomes]
rs7200053	0.82[ASN][1000 genomes]
rs7202596	0.86[ASN][1000 genomes]
rs7204984	0.82[ASN][1000 genomes]
rs7206665	0.82[ASN][1000 genomes]
rs8055490	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8057084	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8063068	0.91[ASN][1000 genomes]
rs977985	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs977987	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9933255	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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	57 gene(s)	inside rSNPs	diseases
10	esv3485939	chr16:75497453-75550284	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3485940	chr16:75497453-75550284	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv572980	chr16:75505046-75549885	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv3313995	chr16:75512166-75566404	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv3313996	chr16:75512166-75566404	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2738809	RP11-252K23.2	cis	Artery Tibial	GTEx
rs2738809	RP11-252K23.2	cis	lung	GTEx
rs2738809	RP11-252K23.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2738809	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs2738809	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs2738809	RP11-252K23.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75498800-75518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:75499200-75519600	Weak transcription	Fetal Intestine Small	intestine
3	chr16:75502400-75518200	Weak transcription	Aorta	Aorta
4	chr16:75506200-75517000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr16:75506800-75520400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr16:75507000-75517600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:75507000-75525600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:75512200-75517000	Weak transcription	Spleen	Spleen
9	chr16:75512600-75525600	Weak transcription	Brain Angular Gyrus	brain
10	chr16:75512800-75516800	Weak transcription	Esophagus	oesophagus
11	chr16:75513600-75523400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr16:75513800-75517400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr16:75514000-75516800	Weak transcription	Brain Anterior Caudate	brain
14	chr16:75514000-75519800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:75514000-75520800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr16:75514000-75522800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:75514000-75523400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr16:75514000-75524800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:75514000-75525400	Weak transcription	Brain Hippocampus Middle	brain
20	chr16:75514000-75528000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr16:75514000-75528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:75514200-75520000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:75514200-75520600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:75514200-75522800	Weak transcription	Brain Substantia Nigra	brain
25	chr16:75514200-75525600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr16:75515200-75520600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:75515600-75516800	Enhancers	Hela-S3	cervix
28	chr16:75515800-75520400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:75515800-75520600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr16:75516000-75517000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:75516000-75519600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:75516000-75521000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr16:75516200-75516800	Enhancers	Fetal Muscle Trunk	muscle
34	chr16:75516200-75521200	Enhancers	NHEK	skin
35	chr16:75516400-75521200	Enhancers	HMEC	breast
36	chr16:75516600-75521200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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