Variant report

Variant	rs2959011
Chromosome Location	chr15:74611781-74611782
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74607660..74609558-chr15:74611685..74613599,2	MCF-7	breast:
2	chr15:74500084..74502169-chr15:74610783..74612337,2	K562	blood:

Variant related genes	Relation type
ENSG00000137868	Chromatin interaction

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

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

rs_ID	r²[population]
rs11072478	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632698	0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11634685	0.92[MEX][hapmap]
rs11635047	0.88[CEU][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs11638442	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12440952	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12900028	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12916765	0.84[EUR][1000 genomes]
rs12917295	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12917557	0.83[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1484216	0.92[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1564782	0.81[CEU][hapmap]
rs1564783	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2277601	0.84[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2277602	0.94[ASW][hapmap];0.81[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs2279356	0.81[CEU][hapmap]
rs2279378	0.96[MEX][hapmap]
rs2415239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899825	0.84[MEX][hapmap]
rs2930291	0.83[MEX][hapmap]
rs2930300	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2930301	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2930302	0.94[ASW][hapmap];0.92[CEU][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2959003	0.87[EUR][1000 genomes]
rs2959004	0.81[CEU][hapmap]
rs2959005	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2959006	0.92[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2959007	0.92[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2959008	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34578565	0.85[EUR][1000 genomes]
rs351184	0.92[MEX][hapmap]
rs351189	0.84[ASN][1000 genomes]
rs4077581	0.80[CEU][hapmap]
rs4887134	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4887135	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs56339065	0.85[EUR][1000 genomes]
rs68021814	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173655	0.86[EUR][1000 genomes]
rs733434	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751527	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751528	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8031121	0.84[CEU][hapmap]
rs900798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs900799	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs900800	0.83[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs900802	0.81[CEU][hapmap]

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	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74604200-74613400	Enhancers	Placenta	Placenta
2	chr15:74604400-74613200	Enhancers	Fetal Thymus	thymus
3	chr15:74604800-74623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:74605200-74613400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:74606200-74612600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:74606200-74613400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:74606400-74613400	Enhancers	Fetal Muscle Leg	muscle
8	chr15:74606600-74613400	Enhancers	Fetal Brain Female	brain
9	chr15:74607000-74613000	Enhancers	Primary hematopoietic stem cells	blood
10	chr15:74607200-74611800	Enhancers	Left Ventricle	heart
11	chr15:74607200-74612000	Enhancers	Right Ventricle	heart
12	chr15:74607200-74612600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:74607200-74613000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:74607200-74613200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:74607200-74613400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:74607400-74613200	Enhancers	Adipose Nuclei	Adipose
17	chr15:74607600-74613400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:74607800-74612000	Enhancers	NHLF	lung
19	chr15:74607800-74613000	Enhancers	Fetal Stomach	stomach
20	chr15:74608000-74612600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:74608000-74613000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:74608200-74613200	Enhancers	GM12878-XiMat	blood
23	chr15:74608400-74613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:74608600-74611800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:74608800-74612200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:74608800-74613200	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:74609200-74613000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:74609600-74612000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:74609600-74612200	Enhancers	Stomach Mucosa	stomach
30	chr15:74609600-74612800	Enhancers	Fetal Intestine Small	intestine
31	chr15:74609600-74613000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr15:74609600-74613200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:74609800-74611800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr15:74609800-74611800	Enhancers	Fetal Lung	lung
35	chr15:74609800-74612400	Enhancers	Placenta Amnion	Placenta Amnion
36	chr15:74609800-74612400	Enhancers	HSMM	muscle
37	chr15:74609800-74612800	Enhancers	Primary B cells from peripheral blood	blood
38	chr15:74609800-74612800	Enhancers	Ovary	ovary
39	chr15:74609800-74613000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr15:74609800-74613000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:74609800-74613200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:74610000-74612000	Enhancers	Right Atrium	heart
43	chr15:74610000-74612400	Enhancers	Brain Anterior Caudate	brain
44	chr15:74610400-74611800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:74610400-74612200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:74610600-74611800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:74610600-74612000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:74610600-74612400	Enhancers	NHDF-Ad	bronchial
49	chr15:74610600-74612400	Enhancers	Osteobl	bone
50	chr15:74610600-74612600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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