Variant report

Variant	rs17498778
Chromosome Location	chr4:99434834-99434835
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	chr4:99428008..99431537-chr4:99432874..99435399,3	MCF-7	breast:
2	chr4:99429986..99431627-chr4:99434644..99437032,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10489125	1.00[JPT][hapmap]
rs10516433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945713	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554849	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17499015	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17564872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17564998	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699645	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699654	1.00[JPT][hapmap]
rs56221164	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59150136	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60026821	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60947018	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532746	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6817773	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830136	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840239	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6840610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846101	0.90[ASN][1000 genomes]
rs6853079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666585	1.00[JPT][hapmap]
rs7667273	1.00[JPT][hapmap]
rs7667608	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676155	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688849	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689116	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9761395	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99397600-99439400	Weak transcription	Primary B cells from cord blood	blood
2	chr4:99417800-99438600	Weak transcription	Right Atrium	heart
3	chr4:99419600-99436400	Weak transcription	HUVEC	blood vessel
4	chr4:99420200-99435800	Weak transcription	Spleen	Spleen
5	chr4:99420400-99436400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:99420400-99436400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:99425000-99436200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:99431000-99435600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:99431200-99436000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:99431200-99436000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:99431200-99436200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99431200-99439600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:99431200-99443600	Weak transcription	Fetal Brain Male	brain
14	chr4:99431400-99436200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:99431400-99436400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:99431400-99436600	Weak transcription	Brain Germinal Matrix	brain
17	chr4:99431600-99435600	Weak transcription	K562	blood
18	chr4:99431600-99436000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:99431600-99436600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:99431800-99438600	Weak transcription	Stomach Mucosa	stomach
21	chr4:99432000-99435800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:99432200-99435600	Weak transcription	Fetal Thymus	thymus
23	chr4:99432200-99435800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:99432200-99435800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:99432200-99436200	Weak transcription	HSMM	muscle
26	chr4:99432200-99436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:99432200-99438600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:99432400-99435800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:99432400-99435800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:99432400-99436400	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:99432400-99437000	Weak transcription	HSMMtube	muscle
32	chr4:99432600-99435600	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:99432600-99435600	Weak transcription	NH-A	brain
34	chr4:99432600-99436400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:99432600-99436400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:99432600-99436400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:99432600-99436400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:99432600-99436400	Weak transcription	Fetal Stomach	stomach
39	chr4:99432600-99436600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:99432600-99438000	Weak transcription	Thymus	Thymus
41	chr4:99432800-99435600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:99432800-99435600	Weak transcription	Fetal Lung	lung
43	chr4:99432800-99435600	Weak transcription	NHLF	lung
44	chr4:99432800-99435800	Weak transcription	Osteobl	bone
45	chr4:99432800-99436000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:99432800-99436400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:99432800-99436400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:99432800-99436400	Weak transcription	Dnd41	blood
49	chr4:99432800-99436600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:99432800-99436800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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