Variant report

Variant	rs9893254
Chromosome Location	chr17:18198948-18198949
allele	C/T
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	POLR2A	chr17:18198805-18198984	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18162298..18165482-chr17:18198310..18200966,3	MCF-7	breast:

Variant related genes	Relation type
TOP3A	TF binding region
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11540888	1.00[ASN][1000 genomes]
rs11870681	1.00[ASN][1000 genomes]
rs16961058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961112	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125154	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28671051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924848	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925170	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925175	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925180	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55973639	1.00[ASN][1000 genomes]
rs61753153	1.00[ASN][1000 genomes]
rs6502648	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7215491	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7222589	1.00[ASN][1000 genomes]
rs73980813	1.00[ASN][1000 genomes]
rs73980819	1.00[ASN][1000 genomes]
rs73980849	1.00[ASN][1000 genomes]
rs73980856	1.00[ASN][1000 genomes]
rs73980857	1.00[ASN][1000 genomes]
rs8074858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080285	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8082574	1.00[ASN][1000 genomes]
rs9894005	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9902011	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9902498	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9903235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903762	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915858	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
3	chr17:18173000-18199000	Strong transcription	Primary T cells from cord blood	blood
4	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
7	chr17:18173400-18200200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:18173400-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr17:18173400-18201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:18173400-18201000	Strong transcription	Fetal Intestine Small	intestine
11	chr17:18173600-18200200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:18173600-18200800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:18174000-18200600	Strong transcription	Dnd41	blood
14	chr17:18174200-18200600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr17:18174800-18200600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:18175600-18200800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:18175800-18199000	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr17:18175800-18200800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:18175800-18201000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:18176200-18200800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:18176400-18199000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:18176400-18200200	Strong transcription	Fetal Intestine Large	intestine
23	chr17:18176400-18200200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr17:18176400-18201000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr17:18176600-18200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:18176600-18200800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:18181200-18200800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr17:18181400-18200200	Strong transcription	Fetal Muscle Leg	muscle
29	chr17:18183000-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:18183400-18200800	Strong transcription	Fetal Brain Female	brain
31	chr17:18183600-18207000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:18184400-18199000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr17:18184600-18201000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr17:18185200-18200000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:18185200-18200200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:18189000-18202800	Weak transcription	Stomach Mucosa	stomach
38	chr17:18190200-18200200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:18191600-18200200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:18192000-18200200	Strong transcription	Brain Anterior Caudate	brain
41	chr17:18193000-18200200	Strong transcription	Hela-S3	cervix
42	chr17:18193800-18204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:18194400-18202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr17:18194600-18202600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:18194600-18202600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr17:18194600-18208000	Weak transcription	Fetal Brain Male	brain
47	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
48	chr17:18195800-18209600	Weak transcription	Psoas Muscle	Psoas
49	chr17:18196000-18202600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:18196000-18204200	Weak transcription	Small Intestine	intestine

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