Variant report

Variant	rs11896140
Chromosome Location	chr2:10282147-10282148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10260565..10262183-chr2:10281401..10283341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10172702	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179663	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179866	0.81[ASN][1000 genomes]
rs10192090	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197121	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10202672	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10209383	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754955	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1130609	0.81[JPT][hapmap]
rs12692399	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12987867	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13009708	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13010608	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028656	0.86[ASN][1000 genomes]
rs13398833	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420725	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16855510	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110642	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160190	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241113	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357465	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357466	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357467	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4668664	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4669531	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432064	0.81[JPT][hapmap]
rs6432066	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432067	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432069	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432070	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6706570	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707144	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707406	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6709408	0.94[ASN][1000 genomes]
rs6715077	0.96[ASN][1000 genomes]
rs6749325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6758411	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759180	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs717886	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs718215	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs729917	0.87[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7420698	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566175	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605457	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv873634	chr2:10275814-10337034	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10263800-10283600	Weak transcription	Spleen	Spleen
2	chr2:10265400-10284000	Weak transcription	Placenta	Placenta
3	chr2:10269600-10299400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:10269800-10285200	Weak transcription	Brain Germinal Matrix	brain
5	chr2:10271400-10303800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:10272200-10284000	Weak transcription	GM12878-XiMat	blood
7	chr2:10272600-10289800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:10273400-10285000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:10273600-10282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:10273600-10283400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:10273800-10282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:10273800-10282600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:10273800-10283200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:10273800-10283400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:10273800-10283400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:10273800-10289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:10273800-10330400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:10274000-10299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:10275200-10284200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:10276400-10307400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:10276600-10284200	Weak transcription	NHLF	lung
22	chr2:10276600-10301800	Weak transcription	Osteobl	bone
23	chr2:10277200-10283400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:10277600-10282800	Weak transcription	Fetal Intestine Large	intestine
25	chr2:10277600-10283400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:10277600-10284000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:10277600-10321600	Weak transcription	K562	blood
28	chr2:10277800-10295400	Weak transcription	Hela-S3	cervix
29	chr2:10278000-10282400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:10278000-10283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:10278000-10302200	Weak transcription	HSMM	muscle
32	chr2:10278000-10311800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:10278200-10285000	Weak transcription	NHEK	skin
34	chr2:10278200-10285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:10279200-10282400	Genic enhancers	Dnd41	blood
36	chr2:10279400-10292000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:10279600-10295600	Weak transcription	Fetal Brain Female	brain
38	chr2:10280400-10283000	Genic enhancers	Fetal Thymus	thymus
39	chr2:10280800-10287000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:10281000-10282400	Genic enhancers	Thymus	Thymus
41	chr2:10281000-10282600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr2:10281000-10282800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:10281000-10283600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:10281000-10292400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:10281000-10294200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:10281200-10282400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:10281200-10282600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:10281200-10283000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:10281200-10283000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:10281400-10282800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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