Variant report

Variant	rs161732
Chromosome Location	chr5:98277122-98277123
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr5:98277012-98277476	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:98277003-98278079	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr5:98276996-98277495	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:98275181-98279858	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr5:98277041-98277434	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:98272097..98275128-chr5:98275593..98280478,6	MCF-7	breast:
2	chr5:98276533..98278644-chr5:98288923..98290589,2	K562	blood:
3	chr5:98269604..98273895-chr5:98275576..98277950,6	K562	blood:
4	chr5:98275762..98278033-chr5:98288005..98290423,2	K562	blood:
5	chr5:98276177..98277799-chr5:98286832..98289590,2	MCF-7	breast:
6	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200351	TF binding region
ENSG00000241597	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10040066	1.00[CHB][hapmap]
rs10050804	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10479348	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11242567	1.00[CHB][hapmap]
rs11242574	0.85[AMR][1000 genomes]
rs11745405	0.84[AMR][1000 genomes]
rs12515042	0.85[AMR][1000 genomes]
rs13179812	1.00[CHB][hapmap]
rs1472622	1.00[CHB][hapmap]
rs150935	0.82[YRI][hapmap]
rs151102	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1604450	0.85[AMR][1000 genomes]
rs161729	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs161730	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs161731	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs161734	0.83[TSI][hapmap]
rs161736	0.83[CEU][hapmap]
rs161739	0.87[ASW][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs161746	0.82[YRI][hapmap]
rs161749	0.83[TSI][hapmap]
rs161750	0.82[YRI][hapmap]
rs161935	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs161936	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs161940	0.87[ASW][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs161943	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161947	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs162337	0.84[ASN][1000 genomes]
rs167798	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1875529	1.00[CHB][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs2221268	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs2447826	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs246251	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545680	0.82[YRI][hapmap]
rs2545735	0.82[YRI][hapmap]
rs2578576	0.82[YRI][hapmap]
rs2578577	0.82[YRI][hapmap]
rs2662256	0.82[YRI][hapmap]
rs325195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325199	0.82[YRI][hapmap]
rs325203	0.87[ASW][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs325204	0.87[ASW][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs325208	0.82[YRI][hapmap]
rs325220	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs326480	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs326481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326482	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs327807	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs331542	0.82[YRI][hapmap]
rs34488	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34489	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs34496	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs34498	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34499	0.84[ASN][1000 genomes]
rs366353	1.00[CHB][hapmap]
rs39660	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs40075	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs428836	0.84[ASN][1000 genomes]
rs4343864	0.85[AMR][1000 genomes]
rs4565239	1.00[CHB][hapmap]
rs4583911	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs467728	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs469018	0.84[ASN][1000 genomes]
rs4703345	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs539024	1.00[CHB][hapmap]
rs6878136	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs709386	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs709387	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs709388	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs709389	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7449447	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7719562	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs7719649	0.85[AMR][1000 genomes]
rs7723242	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs819227	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs819230	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs819231	0.87[AMR][1000 genomes];0.86[EUR][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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
2	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
4	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:98272200-98277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:98272400-98278000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:98272600-98277200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:98272600-98278600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:98272800-98277400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:98273600-98277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:98274000-98277200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr5:98274600-98280000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:98274800-98277400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:98274800-98278800	Weak transcription	HepG2	liver
16	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
18	chr5:98275400-98277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:98275600-98277200	Enhancers	NHDF-Ad	bronchial
20	chr5:98275800-98277200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:98275800-98277200	Enhancers	Brain Anterior Caudate	brain
22	chr5:98275800-98277400	Enhancers	Brain Substantia Nigra	brain
23	chr5:98275800-98277600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:98275800-98277800	Enhancers	Colon Smooth Muscle	Colon
25	chr5:98276000-98277200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:98276000-98277200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:98276000-98277200	Enhancers	Adipose Nuclei	Adipose
28	chr5:98276000-98277200	Enhancers	Fetal Lung	lung
29	chr5:98276000-98277200	Enhancers	Osteobl	bone
30	chr5:98276000-98278000	Enhancers	Fetal Muscle Leg	muscle
31	chr5:98276000-98278600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr5:98276200-98277200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr5:98276200-98277200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:98276200-98277200	Enhancers	Fetal Heart	heart
35	chr5:98276200-98277200	Enhancers	Psoas Muscle	Psoas
36	chr5:98276200-98277200	Enhancers	HSMMtube	muscle
37	chr5:98276200-98277200	Enhancers	NHLF	lung
38	chr5:98276200-98277400	Enhancers	Brain Angular Gyrus	brain
39	chr5:98276200-98277400	Enhancers	Brain Hippocampus Middle	brain
40	chr5:98276200-98277400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:98276200-98277600	Enhancers	Stomach Smooth Muscle	stomach
42	chr5:98276200-98278200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:98276200-98278800	Enhancers	Primary B cells from cord blood	blood
44	chr5:98276200-98281600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:98276400-98277200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:98276400-98277200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:98276400-98277200	Enhancers	Small Intestine	intestine
48	chr5:98276400-98277400	Enhancers	Ovary	ovary
49	chr5:98276400-98277600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr5:98276400-98277600	Enhancers	Left Ventricle	heart

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