Variant report

Variant	rs2065998
Chromosome Location	chr14:55868022-55868023
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	chr14:55868020..55869750-chr14:55873508..55875755,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10130894	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10134937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135891	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];1.00[ASN][1000 genomes]
rs10138838	0.86[EUR][1000 genomes]
rs10140902	0.80[AMR][1000 genomes]
rs10144869	1.00[EUR][1000 genomes]
rs10146943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10149926	1.00[EUR][1000 genomes]
rs10162552	1.00[EUR][1000 genomes]
rs10220441	0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10483640	0.86[EUR][1000 genomes]
rs11844441	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851023	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs13379398	1.00[EUR][1000 genomes]
rs13379420	1.00[EUR][1000 genomes]
rs17128323	0.86[EUR][1000 genomes]
rs17128370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs17128434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17128438	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2050669	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];0.95[ASN][1000 genomes]
rs2341536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379450	1.00[EUR][1000 genomes]
rs28661252	1.00[EUR][1000 genomes]
rs28787988	0.87[EUR][1000 genomes]
rs28883964	0.87[EUR][1000 genomes]
rs56042503	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57612384	0.87[EUR][1000 genomes]
rs59155162	0.87[EUR][1000 genomes]
rs60023093	0.86[EUR][1000 genomes]
rs60204830	0.86[EUR][1000 genomes]
rs61662514	1.00[EUR][1000 genomes]
rs7142831	0.86[EUR][1000 genomes]
rs7145502	0.86[EUR][1000 genomes]
rs7147172	0.87[EUR][1000 genomes]
rs7148663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7153958	0.87[EUR][1000 genomes]
rs7155704	0.86[EUR][1000 genomes]
rs7155729	0.86[EUR][1000 genomes]
rs7160642	0.86[EUR][1000 genomes]
rs7160753	0.86[EUR][1000 genomes]
rs74050958	0.86[EUR][1000 genomes]
rs74050963	1.00[EUR][1000 genomes]
rs74050968	0.87[EUR][1000 genomes]
rs74050975	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74053904	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8007038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016444	0.86[EUR][1000 genomes]
rs8016716	0.86[EUR][1000 genomes]
rs8021377	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323282	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs946058	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9652341	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
4	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55818200-55877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:55836800-55877800	Weak transcription	Esophagus	oesophagus
3	chr14:55848600-55876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:55849200-55876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:55849200-55878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:55850000-55868400	Weak transcription	Right Ventricle	heart
7	chr14:55851000-55871000	Weak transcription	Pancreas	Pancrea
8	chr14:55852000-55877200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr14:55853000-55877200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr14:55854000-55868400	Weak transcription	Gastric	stomach
11	chr14:55854200-55871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:55854800-55878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:55856200-55868600	Weak transcription	Psoas Muscle	Psoas
14	chr14:55856200-55876200	Weak transcription	Fetal Brain Male	brain
15	chr14:55856200-55878000	Weak transcription	Spleen	Spleen
16	chr14:55856400-55870400	Weak transcription	GM12878-XiMat	blood
17	chr14:55856400-55876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:55856400-55877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr14:55856600-55869800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr14:55856600-55876600	Weak transcription	Fetal Brain Female	brain
21	chr14:55856800-55875600	Weak transcription	Dnd41	blood
22	chr14:55856800-55877200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:55859200-55874200	Weak transcription	Fetal Stomach	stomach
24	chr14:55860600-55877800	Weak transcription	Lung	lung
25	chr14:55862000-55876000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr14:55862000-55876200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr14:55862000-55876400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:55862000-55876800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:55862200-55873600	Weak transcription	Fetal Intestine Small	intestine
30	chr14:55862200-55876200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr14:55862200-55876400	Weak transcription	Brain Germinal Matrix	brain
32	chr14:55862200-55877000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr14:55862200-55877600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:55862400-55876200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:55862400-55876200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:55862400-55877200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr14:55862600-55877400	Weak transcription	Fetal Thymus	thymus
38	chr14:55862800-55876000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:55862800-55876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr14:55862800-55877200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:55863400-55868200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr14:55863400-55876600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:55863400-55876600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr14:55863400-55877600	Weak transcription	Placenta	Placenta
45	chr14:55863600-55877400	Weak transcription	Thymus	Thymus
46	chr14:55863800-55876600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr14:55864000-55868400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr14:55864000-55871000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr14:55864000-55871200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr14:55864000-55874400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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