Variant report

Variant	rs11149812
Chromosome Location	chr16:75323645-75323646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75322643-75323672	HUVEC	blood vessel:	n/a	n/a
2	JUND	chr16:75322973-75323651	HCT-116	colon:	n/a	chr16:75323277-75323287 chr16:75323276-75323287 chr16:75323277-75323287 chr16:75323353-75323362 chr16:75323279-75323290 chr16:75323278-75323286 chr16:75323276-75323288

No.	Distal block	Cell Line	Cell type
1	chr16:75323194..75324994-chr16:75337931..75340370,2	MCF-7	breast:
2	chr16:75322113..75324158-chr16:75324406..75326106,2	MCF-7	breast:
3	chr16:75322651..75324699-chr16:75331151..75332861,2	MCF-7	breast:
4	chr16:75298337..75302151-chr16:75321880..75325464,5	MCF-7	breast:

Variant related genes	Relation type
RNU6-758P	TF binding region
ENSG00000153774	Chromatin interaction
ENSG00000050820	Chromatin interaction

Extended variants
information (count: 166 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs1011121	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1017239	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10514393	0.87[CHB][hapmap]
rs10514396	0.83[CHB][hapmap]
rs1074961	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10781976	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10781977	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10871307	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10871308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1109342	0.82[CHB][hapmap]
rs11149813	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11149814	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11149815	0.81[CHB][hapmap]
rs11149816	0.90[ASN][1000 genomes]
rs11149831	0.83[CHB][hapmap]
rs11640018	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11641532	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs11645691	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs11646418	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11646677	0.83[CHB][hapmap]
rs12149063	0.83[CHB][hapmap]
rs12444589	0.82[CHB][hapmap]
rs12445188	0.93[ASN][1000 genomes]
rs12445211	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12445813	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs12446903	0.88[ASN][1000 genomes]
rs12449177	0.98[ASN][1000 genomes]
rs12932952	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12933281	0.81[CHB][hapmap]
rs12935329	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12935787	0.80[ASN][1000 genomes]
rs1364078	0.82[CHB][hapmap]
rs1549306	0.82[CHB][hapmap]
rs1559339	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs17685540	0.81[ASN][1000 genomes]
rs17696696	0.82[CHB][hapmap]
rs17696749	0.83[CHB][hapmap]
rs185052	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs1862705	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1862706	0.82[CHB][hapmap]
rs1895489	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1895490	0.83[CHB][hapmap]
rs2032926	0.91[ASN][1000 genomes]
rs2059256	0.82[CHB][hapmap]
rs2059257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161648	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2161684	0.81[CHB][hapmap]
rs2242405	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs247423	0.85[ASN][1000 genomes]
rs247424	0.84[ASN][1000 genomes]
rs247425	0.84[ASN][1000 genomes]
rs247427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs247431	0.88[ASN][1000 genomes]
rs247434	0.87[ASN][1000 genomes]
rs247436	0.88[ASN][1000 genomes]
rs247437	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247447	1.00[CEU][hapmap]
rs2865527	0.85[ASN][1000 genomes]
rs2865530	0.82[CHB][hapmap]
rs2865531	0.82[CHB][hapmap]
rs2865532	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2903033	0.82[CHB][hapmap]
rs34029337	0.81[ASN][1000 genomes]
rs34624768	0.80[ASN][1000 genomes]
rs34673655	0.81[ASN][1000 genomes]
rs35263058	0.82[CHB][hapmap]
rs35937717	0.80[ASN][1000 genomes]
rs3743606	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs37602	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs3784936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784937	0.95[ASN][1000 genomes]
rs3844219	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851736	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146809	0.82[CHB][hapmap]
rs4146810	0.83[CHB][hapmap]
rs4243111	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4243112	0.81[ASN][1000 genomes]
rs42472	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap]
rs4536500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs455407	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4638613	0.82[CHB][hapmap]
rs467223	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs467780	0.87[ASN][1000 genomes]
rs468079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887811	0.83[EUR][1000 genomes]
rs4887812	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887813	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887815	0.81[ASN][1000 genomes]
rs4887816	0.81[ASN][1000 genomes]
rs4887823	0.82[CHB][hapmap]
rs4887824	0.83[CHB][hapmap]
rs4887828	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4888369	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888370	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888371	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888372	0.81[ASN][1000 genomes]
rs4888374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888375	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888376	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4888377	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4888378	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs4888379	0.83[CHB][hapmap]
rs4888380	0.86[CHB][hapmap]
rs4888381	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888383	0.83[CHB][hapmap]
rs4888386	0.83[CHB][hapmap]
rs4888387	0.82[CHB][hapmap]
rs4888388	0.83[CHB][hapmap]
rs4888389	0.83[CHB][hapmap]
rs4888393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888394	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888395	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888396	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4888397	0.85[ASN][1000 genomes]
rs4888398	0.88[ASN][1000 genomes]
rs4888405	0.82[CHB][hapmap]
rs4888416	0.83[CHB][hapmap]
rs4888425	0.81[CHB][hapmap]
rs4888430	0.85[CHB][hapmap]
rs4993969	0.82[CHB][hapmap]
rs4993971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564245	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564249	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564256	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7187263	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7188604	0.82[CHB][hapmap]
rs7189407	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7192155	0.88[ASN][1000 genomes]
rs7199132	0.82[CHB][hapmap]
rs7199680	0.85[ASN][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7203157	0.83[CHB][hapmap]
rs7204984	0.81[CHB][hapmap]
rs766521	0.82[CHB][hapmap]
rs766522	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8046109	0.86[CHB][hapmap]
rs8046184	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046416	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs8046949	0.88[ASN][1000 genomes]
rs8047811	0.85[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048816	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8049611	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8050059	0.82[CHB][hapmap]
rs8050662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051611	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051785	0.88[ASN][1000 genomes]
rs8053632	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8055609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs889446	0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs9922008	0.84[CHB][hapmap]
rs9933956	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9934007	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9989421	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	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
4	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	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
7	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11149812	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75301000-75325000	Weak transcription	Liver	Liver
2	chr16:75302000-75324000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:75306200-75325000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr16:75306200-75325200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:75307800-75325400	Weak transcription	Osteobl	bone
6	chr16:75312000-75324400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr16:75313400-75324600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr16:75313400-75325200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr16:75313400-75325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:75313600-75323800	Weak transcription	Ovary	ovary
11	chr16:75313600-75325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr16:75313600-75330400	Weak transcription	Pancreas	Pancrea
13	chr16:75314000-75325000	Weak transcription	Brain Anterior Caudate	brain
14	chr16:75314800-75325400	Weak transcription	Colon Smooth Muscle	Colon
15	chr16:75315000-75335600	Weak transcription	Psoas Muscle	Psoas
16	chr16:75315200-75325200	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:75315200-75326600	Weak transcription	Brain Substantia Nigra	brain
18	chr16:75315400-75325400	Weak transcription	Aorta	Aorta
19	chr16:75316800-75325000	Weak transcription	Brain Germinal Matrix	brain
20	chr16:75316800-75325200	Weak transcription	Primary B cells from cord blood	blood
21	chr16:75317000-75323800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr16:75317000-75325000	Weak transcription	Brain Angular Gyrus	brain
23	chr16:75317000-75325800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:75317000-75335600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:75317200-75325000	Weak transcription	Fetal Brain Female	brain
26	chr16:75317200-75325200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
28	chr16:75318600-75323800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:75318600-75330200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr16:75318800-75325000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:75319200-75324000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:75320200-75325200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr16:75320800-75339000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr16:75321000-75326800	Strong transcription	Fetal Intestine Small	intestine
35	chr16:75321200-75326800	Strong transcription	Fetal Stomach	stomach
36	chr16:75321200-75329000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:75321400-75323800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr16:75321400-75324400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr16:75321600-75324000	Enhancers	Fetal Heart	heart
40	chr16:75321600-75324200	Enhancers	Left Ventricle	heart
41	chr16:75321600-75324200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr16:75321600-75330600	Strong transcription	Fetal Lung	lung
43	chr16:75321800-75323800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:75321800-75324400	Enhancers	HUVEC	blood vessel
45	chr16:75321800-75324600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:75321800-75337600	Weak transcription	A549	lung
47	chr16:75322000-75323800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr16:75322000-75325400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr16:75322000-75332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:75322000-75337600	Strong transcription	Fetal Intestine Large	intestine

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