Variant report

Variant	rs162160
Chromosome Location	chr5:98262809-98262810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:98262784-98262977	SH-SY5Y	brain:	n/a	chr5:98262815-98262824
2	POLR2A	chr5:98262735-98265849	Hela-S3	cervix:	n/a	n/a
3	GABPA	chr5:98262803-98263317	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:98262425-98264148	A549	lung:	n/a	n/a
5	POLR2A	chr5:98262788-98263318	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr5:98262802-98266065	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:98262788-98265865	GM12892	blood:	n/a	n/a
8	GABPA	chr5:98262667-98263500	MCF-7	breast:	n/a	n/a
9	POLR2A	chr5:98262736-98267954	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:98261911-98271717	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr5:98262744-98270017	GM12891	blood:	n/a	n/a
12	POLR2A	chr5:98262705-98266805	PBDE	blood:	n/a	n/a
13	POLR2A	chr5:98262041-98266821	IMR90	lung:	n/a	n/a
14	POLR2A	chr5:98262763-98263284	SK-N-MC	brain:	n/a	n/a
15	MAZ	chr5:98262674-98263567	GM12878	blood:	n/a	n/a
16	ZMIZ1	chr5:98262797-98263570	K562	blood:	n/a	n/a
17	POLR2A	chr5:98262745-98263490	HUVEC	blood vessel:	n/a	n/a
18	GABPA	chr5:98262777-98263341	MCF-7	breast:	n/a	n/a
19	CHD1	chr5:98262479-98266772	IMR90	lung:	n/a	chr5:98263846-98263856 chr5:98265975-98265982 chr5:98264811-98264821 chr5:98264740-98264750
20	REST	chr5:98262425-98265892	H1-neurons	neurons:	n/a	chr5:98263595-98263602 chr5:98264406-98264419 chr5:98263123-98263136 chr5:98263593-98263600 chr5:98263120-98263129
21	GABPA	chr5:98262772-98263364	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr5:98262793-98263391	GM12878	blood:	n/a	n/a
23	MYC	chr5:98262805-98265714	K562	blood:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
24	BCLAF1	chr5:98262785-98263739	GM12878	blood:	n/a	n/a
25	EBF1	chr5:98262639-98263688	GM12878	blood:	n/a	chr5:98262716-98262725
26	POLR2A	chr5:98260830-98273878	K562	blood:	n/a	n/a
27	MXI1	chr5:98262547-98266263	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98262437..98267686-chr5:98287585..98292205,9	K562	blood:
2	chr5:98220770..98224200-chr5:98262773..98266161,4	K562	blood:
3	chr5:90674940..90679357-chr5:98262514..98267275,7	K562	blood:
4	chr5:98262538..98264376-chr5:98385068..98386574,2	K562	blood:
5	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
6	chr5:98220809..98224769-chr5:98261722..98266325,5	K562	blood:
7	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
8	chr5:98237133..98240076-chr5:98262664..98264455,2	K562	blood:
9	chr14:81687040..81687872-chr5:98262679..98263179,2	Hela-S3	cervix:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000248489	TF binding region
ENSG00000153922	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000241597	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10044680	1.00[EUR][1000 genomes]
rs10045317	1.00[EUR][1000 genomes]
rs10046011	1.00[EUR][1000 genomes]
rs10060286	1.00[EUR][1000 genomes]
rs13358830	1.00[EUR][1000 genomes]
rs1382336	1.00[EUR][1000 genomes]
rs161743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162139	1.00[EUR][1000 genomes]
rs162141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162142	1.00[EUR][1000 genomes]
rs162143	1.00[EUR][1000 genomes]
rs162157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162161	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs162162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs170579	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166397	1.00[EUR][1000 genomes]
rs17166450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs179175	1.00[EUR][1000 genomes]
rs1828171	1.00[EUR][1000 genomes]
rs28782775	1.00[EUR][1000 genomes]
rs325196	1.00[AMR][1000 genomes]
rs325198	1.00[EUR][1000 genomes]
rs325210	1.00[AMR][1000 genomes]
rs325216	1.00[EUR][1000 genomes]
rs327801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327805	1.00[EUR][1000 genomes]
rs451883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57969582	1.00[EUR][1000 genomes]
rs59156696	1.00[EUR][1000 genomes]
rs61578983	1.00[EUR][1000 genomes]
rs6891520	1.00[EUR][1000 genomes]
rs73151499	1.00[EUR][1000 genomes]
rs73153514	1.00[EUR][1000 genomes]
rs73153532	1.00[EUR][1000 genomes]
rs73155421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73155423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7727696	1.00[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus
3	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
4	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:98236600-98263000	Weak transcription	Ovary	ovary
6	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:98255200-98263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:98260000-98263000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:98260000-98263000	Weak transcription	Gastric	stomach
13	chr5:98260000-98263000	Weak transcription	Pancreas	Pancrea
14	chr5:98260000-98263600	Weak transcription	Spleen	Spleen
15	chr5:98260400-98263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:98260600-98263000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:98260600-98263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:98260600-98263000	Weak transcription	Lung	lung
19	chr5:98261200-98263000	Weak transcription	Small Intestine	intestine
20	chr5:98261200-98266000	Active TSS	Thymus	Thymus
21	chr5:98261600-98263000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:98261600-98263000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:98261600-98263000	Weak transcription	Left Ventricle	heart
24	chr5:98261600-98263000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:98261600-98265800	Active TSS	GM12878-XiMat	blood
26	chr5:98261600-98266200	Active TSS	Fetal Thymus	thymus
27	chr5:98261800-98263000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:98261800-98266200	Active TSS	K562	blood
29	chr5:98262000-98263200	Flanking Active TSS	Dnd41	blood
30	chr5:98262000-98266000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:98262000-98266000	Active TSS	A549	lung
32	chr5:98262200-98263000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr5:98262200-98263000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr5:98262200-98263000	Weak transcription	Placenta	Placenta
35	chr5:98262200-98263200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:98262200-98263200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr5:98262200-98263200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:98262200-98263600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:98262200-98265600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr5:98262200-98265800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:98262200-98265800	Active TSS	HMEC	breast
44	chr5:98262200-98266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr5:98262400-98263000	Flanking Active TSS	HepG2	liver
46	chr5:98262400-98263400	Flanking Active TSS	HUVEC	blood vessel
47	chr5:98262400-98263600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:98262400-98263600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:98262400-98264600	Active TSS	Right Atrium	heart
50	chr5:98262400-98265800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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