Variant report

Variant	rs12798689
Chromosome Location	chr11:101301836-101301837
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:101296877..101299041-chr11:101301262..101303756,2	MCF-7	breast:
2	chr11:101299826..101304335-chr11:101307356..101314246,9	MCF-7	breast:
3	chr11:100997015..100999242-chr11:101300083..101302474,2	MCF-7	breast:
4	chr11:100992008..101001878-chr11:101300412..101311512,29	MCF-7	breast:
5	chr11:101299708..101303554-chr11:101304150..101306716,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10458946	0.94[EUR][1000 genomes]
rs10791460	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10791461	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10895107	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11224728	0.81[EUR][1000 genomes]
rs11224729	0.81[EUR][1000 genomes]
rs11224748	0.90[EUR][1000 genomes]
rs11224752	0.94[EUR][1000 genomes]
rs11224753	0.94[EUR][1000 genomes]
rs11224754	0.94[EUR][1000 genomes]
rs11224755	0.94[EUR][1000 genomes]
rs11224756	0.94[EUR][1000 genomes]
rs11224758	0.94[EUR][1000 genomes]
rs11224764	0.87[YRI][hapmap]
rs11224766	0.87[YRI][hapmap]
rs11532049	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12221599	0.91[ASN][1000 genomes]
rs12225785	0.89[ASN][1000 genomes]
rs12226619	0.99[ASN][1000 genomes]
rs12273188	0.92[YRI][hapmap]
rs12785425	0.92[ASN][1000 genomes]
rs12789079	0.94[ASN][1000 genomes]
rs12791134	0.81[AMR][1000 genomes]
rs12794328	0.84[CHB][hapmap]
rs12795350	0.83[EUR][1000 genomes]
rs12795968	0.94[EUR][1000 genomes]
rs12796333	0.94[EUR][1000 genomes]
rs12797860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12798288	0.94[EUR][1000 genomes]
rs12802904	0.94[EUR][1000 genomes]
rs12803560	0.94[EUR][1000 genomes]
rs12803803	0.94[EUR][1000 genomes]
rs12803811	0.94[EUR][1000 genomes]
rs1938972	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1938987	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1938989	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1938990	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1938991	0.94[EUR][1000 genomes]
rs1938994	0.84[EUR][1000 genomes]
rs2508354	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508357	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508358	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508359	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2508360	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2508362	0.90[EUR][1000 genomes]
rs2508365	0.91[EUR][1000 genomes]
rs2508366	0.91[EUR][1000 genomes]
rs2508367	0.91[EUR][1000 genomes]
rs2508368	0.85[EUR][1000 genomes]
rs2508369	0.91[EUR][1000 genomes]
rs2508371	0.91[EUR][1000 genomes]
rs2508372	0.91[EUR][1000 genomes]
rs2508375	0.91[EUR][1000 genomes]
rs2513146	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2513149	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2513150	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2513151	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513152	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513153	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513154	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513168	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2513169	0.91[EUR][1000 genomes]
rs2513170	0.91[EUR][1000 genomes]
rs2513172	0.90[EUR][1000 genomes]
rs2513174	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2513175	0.91[EUR][1000 genomes]
rs2513176	0.91[EUR][1000 genomes]
rs2513178	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3016236	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3018696	0.91[EUR][1000 genomes]
rs3018699	0.85[AMR][1000 genomes]
rs34681694	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35180268	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35452558	0.94[EUR][1000 genomes]
rs4520564	0.82[CHB][hapmap]
rs56380147	0.94[AFR][1000 genomes]
rs6590854	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6590855	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66975288	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7108099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7121801	0.91[EUR][1000 genomes]
rs744021	0.94[EUR][1000 genomes]
rs7926811	0.91[EUR][1000 genomes]
rs7938688	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7939471	0.91[EUR][1000 genomes]
rs7948589	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7948940	0.93[YRI][hapmap]
rs7951897	0.90[YRI][hapmap]
rs7952146	0.90[YRI][hapmap]
rs9795186	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	esv2753322	chr11:101052790-101311790	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv468851	chr11:101268447-101330807	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv556132	chr11:101268447-101330807	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101299800-101302000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr11:101299800-101303200	Enhancers	Placenta	Placenta
3	chr11:101299800-101304000	Enhancers	Ovary	ovary
4	chr11:101300000-101302000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr11:101300000-101302000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:101300000-101302200	Enhancers	Rectal Smooth Muscle	rectum
7	chr11:101300000-101307600	Enhancers	Fetal Lung	lung
8	chr11:101300200-101302000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr11:101300600-101302000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:101300800-101302000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr11:101300800-101302000	Enhancers	Fetal Stomach	stomach
12	chr11:101301000-101302000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:101301000-101302000	Enhancers	NHLF	lung
14	chr11:101301000-101303600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:101301200-101302000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:101301200-101302000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr11:101301200-101302600	Weak transcription	Stomach Mucosa	stomach
18	chr11:101301200-101306200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:101301400-101302000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr11:101301400-101302000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr11:101301400-101302000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr11:101301400-101302000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:101301400-101302200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:101301400-101302200	Enhancers	Colon Smooth Muscle	Colon
25	chr11:101301400-101302200	Enhancers	HMEC	breast
26	chr11:101301400-101302200	Enhancers	NHEK	skin
27	chr11:101301600-101302000	Enhancers	NH-A	brain
28	chr11:101301600-101303600	Weak transcription	Fetal Brain Male	brain
29	chr11:101301800-101302000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr11:101301800-101302000	Enhancers	Osteobl	bone
31	chr11:101301800-101302200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:101301800-101302200	Enhancers	HSMM	muscle

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