Variant report

Variant	rs2878800
Chromosome Location	chr11:9772368-9772369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9526683..9529040-chr11:9771305..9773861,2	K562	blood:
2	chr11:9634169..9637157-chr11:9770583..9773571,2	MCF-7	breast:
3	chr11:9405010..9406723-chr11:9771415..9773442,2	MCF-7	breast:
4	chr11:9589955..9591769-chr11:9771252..9773790,2	MCF-7	breast:
5	chr11:9634797..9636840-chr11:9770227..9772919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205339	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1045634	0.85[JPT][hapmap]
rs1056593	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs1056674	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770061	0.85[JPT][hapmap]
rs10840300	0.80[JPT][hapmap]
rs11042498	0.85[JPT][hapmap]
rs11042562	1.00[CEU][hapmap]
rs11821544	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11821692	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11825952	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11828354	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1496475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16906967	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16907071	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs1845884	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607967	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3197265	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34696762	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751001	1.00[CEU][hapmap]
rs3763862	0.85[JPT][hapmap]
rs3817010	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829252	0.85[JPT][hapmap]
rs4910500	0.85[JPT][hapmap]
rs55959510	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56029305	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56096143	0.81[ASN][1000 genomes]
rs56340721	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57070018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57590863	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57650149	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57843161	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57864531	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58073079	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58217715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58765157	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59070186	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60195226	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60544361	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60548107	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60601382	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60929104	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61059316	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61284089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61469272	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483649	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483650	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483651	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483654	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483655	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6483658	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7113055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7928407	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935267	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7936721	0.85[JPT][hapmap]
rs7939896	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940708	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7940826	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7946920	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949343	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950075	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868860	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868861	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868862	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9742200-9779400	Weak transcription	Fetal Brain Male	brain
2	chr11:9745000-9775600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:9755000-9777600	Weak transcription	Colonic Mucosa	Colon
4	chr11:9757600-9774600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:9758800-9776000	Weak transcription	Brain Germinal Matrix	brain
6	chr11:9761000-9777200	Weak transcription	Fetal Kidney	kidney
7	chr11:9762400-9777200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:9762400-9777400	Weak transcription	Esophagus	oesophagus
9	chr11:9762400-9777400	Weak transcription	Right Ventricle	heart
10	chr11:9762400-9779400	Weak transcription	Liver	Liver
11	chr11:9762400-9779400	Weak transcription	Psoas Muscle	Psoas
12	chr11:9762600-9779200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:9762800-9779400	Weak transcription	Fetal Brain Female	brain
14	chr11:9763200-9773600	Weak transcription	HepG2	liver
15	chr11:9763200-9775200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:9763600-9779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:9764400-9773800	Weak transcription	Thymus	Thymus
18	chr11:9764800-9774000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:9766200-9774000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:9766400-9774000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:9766800-9774000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:9768800-9774200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:9769400-9772600	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:9770000-9772800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:9770200-9772600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:9770200-9773400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:9770200-9773600	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr11:9770200-9773600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:9770200-9774000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:9770200-9774000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:9770200-9774000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:9770200-9774200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:9770200-9774200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:9770200-9774200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:9770200-9774200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:9770200-9775400	Weak transcription	Right Atrium	heart
37	chr11:9770200-9775800	Weak transcription	Brain Angular Gyrus	brain
38	chr11:9770200-9776400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:9770200-9777000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:9770200-9777000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:9770200-9777600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:9770200-9777600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:9770200-9779200	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:9770200-9779400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:9770200-9779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:9770200-9779400	Weak transcription	Ovary	ovary
47	chr11:9770200-9779400	Weak transcription	Pancreas	Pancrea
48	chr11:9770200-9779600	Weak transcription	Small Intestine	intestine
49	chr11:9770400-9773000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:9770400-9773600	Weak transcription	K562	blood

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