Variant report

Variant	rs17100694
Chromosome Location	chr1:78005951-78005952
allele	C/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	TCF12	chr1:78004391-78006017	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr1:78005490-78006599	Hela-S3	cervix:	n/a	chr1:78006375-78006384
3	MXI1	chr1:78005731-78006460	Hela-S3	cervix:	n/a	n/a
4	STAT1	chr1:78004728-78006805	Hela-S3	cervix:	n/a	chr1:78006375-78006384
5	CEBPB	chr1:78005674-78006766	A549	lung:	n/a	n/a
6	FOSL2	chr1:78004536-78006029	SK-N-SH	brain:	n/a	chr1:78005610-78005619
7	POLR2A	chr1:78004473-78006648	U87	brain:	n/a	n/a
8	SMARCC1	chr1:78004743-78006663	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr1:78004364-78006643	A549	lung:	n/a	n/a
10	NFIC	chr1:78004540-78006037	SK-N-SH	brain:	n/a	n/a
11	MAX	chr1:78004395-78006031	A549	lung:	n/a	n/a
12	TFAP2C	chr1:78005012-78006925	Hela-S3	cervix:	n/a	n/a
13	PBX3	chr1:78004498-78006058	SK-N-SH	brain:	n/a	n/a
14	JUND	chr1:78004698-78006012	SK-N-SH	brain:	n/a	chr1:78005610-78005619
15	JUND	chr1:78005452-78006624	Hela-S3	cervix:	n/a	chr1:78005610-78005619 chr1:78006376-78006383
16	EP300	chr1:78004662-78006119	SK-N-SH	brain:	n/a	chr1:78005869-78005882
17	GATA3	chr1:78004360-78006650	A549	lung:	n/a	n/a
18	MAFK	chr1:78005431-78006272	Hela-S3	cervix:	n/a	chr1:78005622-78005631 chr1:78005615-78005635 chr1:78005621-78005631 chr1:78005617-78005633
19	SP1	chr1:78004491-78006024	A549	lung:	n/a	chr1:78005493-78005507 chr1:78005328-78005337
20	TBP	chr1:78005461-78006550	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:78004532-78006692	U87	brain:	n/a	n/a
22	CEBPB	chr1:78004592-78006983	Hela-S3	cervix:	n/a	n/a
23	GATA3	chr1:78004581-78005999	SK-N-SH	brain:	n/a	n/a
24	EP300	chr1:78005436-78006603	Hela-S3	cervix:	n/a	chr1:78005869-78005882 chr1:78006398-78006412
25	PBX3	chr1:78004622-78006044	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr1:78004480-78006099	SK-N-SH	brain:	n/a	n/a
27	TCF12	chr1:78004404-78006421	SK-N-SH	brain:	n/a	n/a
28	MAX	chr1:78005343-78006559	Hela-S3	cervix:	n/a	n/a
29	RCOR1	chr1:78004955-78006618	Hela-S3	cervix:	n/a	n/a
30	MAX	chr1:78005368-78005965	SK-N-SH	brain:	n/a	n/a
31	EP300	chr1:78004502-78005957	A549	lung:	n/a	chr1:78005869-78005882
32	RXRA	chr1:78004721-78006071	SK-N-SH	brain:	n/a	n/a
33	RAD21	chr1:78005400-78005951	Hela-S3	cervix:	n/a	n/a
34	TCF7L2	chr1:78005289-78006929	Hela-S3	cervix:	n/a	chr1:78006375-78006384
35	MAX	chr1:78005440-78006542	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:78004477-78006805	U87	brain:	n/a	n/a
37	FOSL2	chr1:78004438-78005999	A549	lung:	n/a	chr1:78005610-78005619
38	MAZ	chr1:78005315-78006414	Hela-S3	cervix:	n/a	n/a
39	SP1	chr1:78004454-78005971	A549	lung:	n/a	chr1:78005493-78005507 chr1:78005328-78005337
40	TFAP2A	chr1:78005423-78006572	Hela-S3	cervix:	n/a	chr1:78005707-78005719
41	POLR2A	chr1:78004471-78006766	U87	brain:	n/a	n/a
42	GTF2F1	chr1:78005487-78006496	Hela-S3	cervix:	n/a	n/a
43	REST	chr1:78005315-78005974	A549	lung:	n/a	n/a
44	EBF1	chr1:78005623-78006540	GM12878	blood:	n/a	chr1:78006303-78006314

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1135921	1.00[AMR][1000 genomes]
rs1353727	1.00[AMR][1000 genomes]
rs17100655	1.00[AMR][1000 genomes]
rs17100731	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100789	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100941	1.00[AMR][1000 genomes]
rs2047167	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2088519	1.00[AMR][1000 genomes]
rs2256679	1.00[AMR][1000 genomes]
rs2291689	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2647491	0.96[AFR][1000 genomes]
rs2647495	1.00[AMR][1000 genomes]
rs2647513	1.00[AMR][1000 genomes]
rs2803137	0.96[AFR][1000 genomes]
rs2803139	1.00[AMR][1000 genomes]
rs2803154	1.00[AMR][1000 genomes]
rs2803166	1.00[AMR][1000 genomes]
rs2803167	1.00[AMR][1000 genomes]
rs2803169	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2803170	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2803171	0.93[AFR][1000 genomes]
rs3104462	1.00[AMR][1000 genomes]
rs3104463	1.00[AMR][1000 genomes]
rs3112830	1.00[AMR][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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
8	chr1:78001400-78006600	Enhancers	NHEK	skin
9	chr1:78001600-78006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:78001600-78006600	Enhancers	HMEC	breast
11	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:78003800-78006000	Enhancers	Fetal Muscle Leg	muscle
13	chr1:78004200-78007800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:78004400-78006000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:78004400-78006200	Enhancers	Stomach Mucosa	stomach
16	chr1:78004400-78006200	Flanking Active TSS	A549	lung
17	chr1:78004400-78006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:78004400-78007600	Enhancers	GM12878-XiMat	blood
19	chr1:78004600-78006000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:78004600-78006000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:78004600-78006000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:78004600-78006000	Enhancers	Brain Substantia Nigra	brain
23	chr1:78004600-78006000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:78004600-78006000	Flanking Active TSS	NH-A	brain
25	chr1:78004600-78006200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:78004600-78006200	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:78004600-78006200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:78004600-78006400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:78004600-78006600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:78004600-78006600	Flanking Active TSS	Osteobl	bone
31	chr1:78004600-78008200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:78004800-78006200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:78004800-78006200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:78004800-78006200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:78004800-78006400	Flanking Active TSS	Hela-S3	cervix
36	chr1:78004800-78006600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:78004800-78007400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr1:78004800-78010800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:78005000-78006000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:78005000-78006000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:78005000-78006000	Enhancers	Brain Hippocampus Middle	brain
42	chr1:78005000-78006200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:78005000-78006200	Enhancers	Gastric	stomach
44	chr1:78005000-78006200	Enhancers	HSMMtube	muscle
45	chr1:78005000-78006400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:78005000-78006600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:78005000-78007400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:78005200-78006200	Enhancers	Lung	lung
49	chr1:78005200-78007400	Enhancers	Placenta	Placenta
50	chr1:78005200-78008000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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