Variant report

Variant	rs17027597
Chromosome Location	chr4:99365213-99365214
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	chr4:99352645..99355637-chr4:99364495..99366451,2	MCF-7	breast:
2	chr4:99181854..99184121-chr4:99363566..99365529,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214559	Chromatin interaction
ENSG00000138698	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10001137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	1.00[EUR][1000 genomes]
rs17027617	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	0.91[AMR][1000 genomes]
rs28494643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.82[AMR][1000 genomes]
rs28503871	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28731135	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56805018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.91[AMR][1000 genomes]
rs60544326	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6831386	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.91[AMR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.82[AMR][1000 genomes]
rs7656868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
2	chr4:99325800-99367000	Weak transcription	Right Ventricle	heart
3	chr4:99334400-99366000	Weak transcription	Psoas Muscle	Psoas
4	chr4:99334400-99367400	Weak transcription	Small Intestine	intestine
5	chr4:99334400-99368800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:99337600-99369800	Weak transcription	Fetal Heart	heart
7	chr4:99339000-99370200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:99340800-99370600	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:99342600-99366600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:99342800-99367400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:99342800-99370000	Weak transcription	Placenta	Placenta
12	chr4:99343000-99368000	Weak transcription	Gastric	stomach
13	chr4:99344200-99366200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:99345000-99367200	Weak transcription	GM12878-XiMat	blood
15	chr4:99346400-99371200	Weak transcription	Fetal Brain Female	brain
16	chr4:99346600-99365600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:99352200-99366800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:99352600-99366200	Weak transcription	NHDF-Ad	bronchial
19	chr4:99353200-99367000	Weak transcription	A549	lung
20	chr4:99355000-99365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:99355000-99366400	Strong transcription	Primary B cells from cord blood	blood
22	chr4:99355200-99365600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:99355400-99365800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:99355400-99366600	Strong transcription	Fetal Thymus	thymus
25	chr4:99355600-99365800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:99355800-99367200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:99356200-99366000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:99356200-99366800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:99356400-99365600	Weak transcription	Esophagus	oesophagus
30	chr4:99356400-99366800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:99356400-99367200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:99356400-99370200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:99356400-99370600	Weak transcription	Fetal Stomach	stomach
34	chr4:99356600-99366600	Weak transcription	Fetal Kidney	kidney
35	chr4:99356800-99370400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:99359200-99366600	Weak transcription	HMEC	breast
37	chr4:99359400-99366200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:99360200-99365400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:99360200-99366000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:99360800-99366200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:99361000-99365600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:99361400-99365600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:99361400-99365800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:99361600-99365600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:99361600-99365800	Strong transcription	Adipose Nuclei	Adipose
46	chr4:99361600-99366800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:99361800-99366800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:99362000-99365600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr4:99362200-99366000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:99362400-99365400	Strong transcription	Primary B cells from peripheral blood	blood

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