Variant report

Variant	rs100912
Chromosome Location	chr16:75519917-75519918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75497139..75499689-chr16:75518408..75520806,2	K562	blood:
2	chr16:75495821..75498564-chr16:75519066..75522748,3	MCF-7	breast:
3	chr16:75514359..75521343-chr16:75549270..75552665,7	MCF-7	breast:
4	chr16:75518580..75520700-chr16:75535226..75539428,3	MCF-7	breast:
5	chr16:75285110..75287717-chr16:75517291..75520144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261717	Chromatin interaction
ENSG00000050820	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000262583	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1030261	0.83[ASN][1000 genomes]
rs1030262	0.85[ASN][1000 genomes]
rs10514393	0.81[JPT][hapmap]
rs10514396	0.86[JPT][hapmap]
rs10871312	0.83[ASN][1000 genomes]
rs10871313	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1109342	0.86[JPT][hapmap]
rs11149815	0.81[JPT][hapmap]
rs11149831	0.86[JPT][hapmap]
rs11640018	0.82[JPT][hapmap]
rs11641249	0.90[ASN][1000 genomes]
rs11641430	0.86[ASN][1000 genomes]
rs11641532	0.81[JPT][hapmap]
rs11643207	0.86[ASN][1000 genomes]
rs11644306	0.84[ASN][1000 genomes]
rs11646677	0.81[JPT][hapmap]
rs11649638	0.83[ASN][1000 genomes]
rs12051137	0.86[ASN][1000 genomes]
rs12149063	0.86[JPT][hapmap]
rs12444589	0.81[JPT][hapmap]
rs12446877	0.86[ASN][1000 genomes]
rs12918797	0.86[ASN][1000 genomes]
rs12924333	0.81[ASN][1000 genomes]
rs12927562	0.83[ASN][1000 genomes]
rs12928036	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12933281	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1364078	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1424013	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1549306	0.86[JPT][hapmap]
rs17696696	0.86[JPT][hapmap]
rs17696749	0.81[JPT][hapmap]
rs17696831	0.86[ASN][1000 genomes]
rs1834013	0.86[ASN][1000 genomes]
rs1834014	0.86[ASN][1000 genomes]
rs1862706	0.85[JPT][hapmap]
rs1895490	0.86[JPT][hapmap]
rs2059256	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2161684	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs247454	0.97[ASN][1000 genomes]
rs2738809	0.95[ASN][1000 genomes]
rs2738812	0.84[ASN][1000 genomes]
rs2738813	0.84[ASN][1000 genomes]
rs2738814	0.87[ASN][1000 genomes]
rs28558946	0.83[ASN][1000 genomes]
rs2865530	0.86[JPT][hapmap]
rs2865531	0.86[JPT][hapmap]
rs28655617	0.82[ASN][1000 genomes]
rs2903033	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3115960	0.94[ASN][1000 genomes]
rs34539062	0.86[ASN][1000 genomes]
rs34918083	0.86[ASN][1000 genomes]
rs34996006	0.80[ASN][1000 genomes]
rs35214308	0.80[ASN][1000 genomes]
rs35263058	0.86[JPT][hapmap]
rs35683383	0.81[ASN][1000 genomes]
rs3743607	0.82[JPT][hapmap]
rs37592	0.86[ASN][1000 genomes]
rs37593	0.86[ASN][1000 genomes]
rs37594	0.86[ASN][1000 genomes]
rs37595	0.86[ASN][1000 genomes]
rs37606	0.90[ASN][1000 genomes]
rs3851733	0.86[JPT][hapmap]
rs3863445	0.86[JPT][hapmap]
rs40446	0.86[ASN][1000 genomes]
rs4146809	0.86[JPT][hapmap]
rs4146810	0.86[JPT][hapmap]
rs4638613	0.86[JPT][hapmap]
rs4887823	0.86[JPT][hapmap]
rs4887824	0.86[JPT][hapmap]
rs4887829	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4888377	0.84[CHB][hapmap]
rs4888378	0.82[JPT][hapmap]
rs4888379	0.86[JPT][hapmap]
rs4888380	0.86[JPT][hapmap]
rs4888383	0.86[JPT][hapmap]
rs4888386	0.86[JPT][hapmap]
rs4888387	0.86[JPT][hapmap]
rs4888388	0.86[JPT][hapmap]
rs4888389	0.86[JPT][hapmap]
rs4888405	0.86[JPT][hapmap]
rs4888415	0.86[JPT][hapmap]
rs4888416	0.86[JPT][hapmap]
rs4888425	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4888426	0.80[ASN][1000 genomes]
rs4888427	0.81[ASN][1000 genomes]
rs4888430	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4888431	0.84[ASN][1000 genomes]
rs4888432	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs4993969	0.81[JPT][hapmap]
rs56116092	0.88[ASN][1000 genomes]
rs59155720	0.81[ASN][1000 genomes]
rs59347518	0.81[ASN][1000 genomes]
rs59465235	0.83[ASN][1000 genomes]
rs62060550	0.86[ASN][1000 genomes]
rs62060551	0.86[ASN][1000 genomes]
rs6564261	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7188604	0.86[JPT][hapmap]
rs7193828	0.87[ASN][1000 genomes]
rs7194035	0.87[ASN][1000 genomes]
rs7195161	0.86[ASN][1000 genomes]
rs7199062	0.80[ASN][1000 genomes]
rs7199132	0.90[JPT][hapmap]
rs7200053	0.80[ASN][1000 genomes]
rs7202596	0.84[ASN][1000 genomes]
rs7203157	0.86[JPT][hapmap]
rs7204984	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7206665	0.80[ASN][1000 genomes]
rs766521	0.86[JPT][hapmap]
rs8046109	0.86[JPT][hapmap]
rs8050059	0.86[JPT][hapmap]
rs8055490	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8057084	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8063068	0.90[ASN][1000 genomes]
rs977985	0.88[ASN][1000 genomes]
rs977987	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9933255	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs100912	RP11-252K23.2	cis	Artery Tibial	GTEx
rs100912	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs100912	CHST6	cis	multi-tissue	Pritchard
rs100912	CHST6	cis	lymphoblastoid	seeQTL
rs100912	RP11-252K23.2	cis	Thyroid	GTEx
rs100912	CFDP1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75506800-75520400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr16:75507000-75525600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:75512600-75525600	Weak transcription	Brain Angular Gyrus	brain
4	chr16:75513600-75523400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr16:75514000-75520800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr16:75514000-75522800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr16:75514000-75523400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr16:75514000-75524800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr16:75514000-75525400	Weak transcription	Brain Hippocampus Middle	brain
10	chr16:75514000-75528000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr16:75514000-75528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr16:75514200-75520000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:75514200-75520600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:75514200-75522800	Weak transcription	Brain Substantia Nigra	brain
15	chr16:75514200-75525600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:75515200-75520600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr16:75515800-75520400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:75515800-75520600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr16:75516000-75521000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr16:75516200-75521200	Enhancers	NHEK	skin
21	chr16:75516400-75521200	Enhancers	HMEC	breast
22	chr16:75516600-75521200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:75517200-75526000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:75517400-75520600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr16:75517400-75522800	Weak transcription	Brain Anterior Caudate	brain
26	chr16:75517600-75520600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:75517600-75521200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:75518200-75520800	Enhancers	Dnd41	blood
29	chr16:75518600-75520000	Enhancers	Primary B cells from cord blood	blood
30	chr16:75519200-75520200	Enhancers	Hela-S3	cervix
31	chr16:75519200-75520800	Enhancers	Esophagus	oesophagus
32	chr16:75519200-75521400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr16:75519400-75521200	Flanking Active TSS	GM12878-XiMat	blood
34	chr16:75519400-75521400	Enhancers	HSMMtube	muscle
35	chr16:75519600-75520200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:75519600-75520200	Enhancers	Duodenum Mucosa	Duodenum
37	chr16:75519600-75520200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr16:75519600-75520800	Enhancers	Placenta	Placenta
39	chr16:75519600-75521400	Enhancers	Fetal Intestine Small	intestine
40	chr16:75519600-75521600	Enhancers	Fetal Intestine Large	intestine
41	chr16:75519800-75520000	Enhancers	Fetal Thymus	thymus
42	chr16:75519800-75520200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr16:75519800-75520200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr16:75519800-75520400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr16:75519800-75520800	Flanking Active TSS	HepG2	liver
46	chr16:75519800-75520800	Enhancers	HSMM	muscle
47	chr16:75519800-75521400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr16:75519800-75521600	Enhancers	Colonic Mucosa	Colon

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