Variant report

Variant	rs16845221
Chromosome Location	chr1:225924178-225924179
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	NR3C1	chr1:225923977-225924511	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
2	GATA2	chr1:225923236-225925427	SH-SY5Y	brain:	n/a	chr1:225923678-225923685 chr1:225924034-225924041
3	MAZ	chr1:225924015-225925557	Hela-S3	cervix:	n/a	n/a
4	NR3C1	chr1:225923951-225924531	ECC-1	luminal epithelium:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
5	CEBPB	chr1:225922960-225925434	Hela-S3	cervix:	n/a	chr1:225924703-225924714 chr1:225923420-225923433 chr1:225924702-225924715 chr1:225924702-225924715 chr1:225923420-225923431 chr1:225923246-225923258
6	MAX	chr1:225923149-225925666	Hela-S3	cervix:	n/a	n/a
7	BRCA1	chr1:225923201-225925446	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr1:225923022-225924263	SK-N-SH	brain:	n/a	chr1:225923678-225923685 chr1:225924034-225924041
9	MAX	chr1:225923173-225924246	A549	lung:	n/a	n/a
10	NFIC	chr1:225923980-225925352	ECC-1	luminal epithelium:	n/a	chr1:225925113-225925129 chr1:225925112-225925129
11	FOS	chr1:225923153-225924188	MCF10A-Er-Src	breast:	n/a	n/a
12	RFX5	chr1:225923152-225925273	Hela-S3	cervix:	n/a	n/a
13	NR3C1	chr1:225923933-225924392	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
14	NR3C1	chr1:225923264-225924639	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225923712-225923719 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
15	NR3C1	chr1:225924033-225924441	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
16	NR3C1	chr1:225924022-225924433	ECC-1	luminal epithelium:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
17	SMC3	chr1:225923090-225925575	Hela-S3	cervix:	n/a	n/a
18	NR3C1	chr1:225923316-225924549	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225923712-225923719 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
19	TCF7L2	chr1:225923022-225925297	Hela-S3	cervix:	n/a	chr1:225924315-225924324 chr1:225924311-225924327 chr1:225924313-225924323 chr1:225924311-225924327 chr1:225924312-225924326
20	SMARCC1	chr1:225923135-225925839	Hela-S3	cervix:	n/a	n/a
21	NR3C1	chr1:225923200-225924598	A549	lung:	n/a	chr1:225924180-225924194 chr1:225924179-225924195 chr1:225924174-225924200 chr1:225924174-225924200 chr1:225923712-225923719 chr1:225924180-225924195 chr1:225924179-225924195 chr1:225924176-225924197 chr1:225924174-225924200 chr1:225924179-225924195 chr1:225924179-225924195
22	KAP1	chr1:225923391-225924306	U2OS	brain:	n/a	n/a
23	PBX3	chr1:225923108-225924444	SK-N-SH	brain:	n/a	n/a
24	NFIC	chr1:225924110-225925488	ECC-1	luminal epithelium:	n/a	chr1:225925113-225925129 chr1:225925112-225925129
25	GATA3	chr1:225922948-225924233	A549	lung:	n/a	chr1:225923678-225923685 chr1:225924034-225924041
26	MAX	chr1:225923069-225924340	A549	lung:	n/a	n/a
27	NFIC	chr1:225924137-225925477	SK-N-SH	brain:	n/a	chr1:225925113-225925129 chr1:225925112-225925129
28	EP300	chr1:225922991-225924534	A549	lung:	n/a	chr1:225923629-225923636 chr1:225924362-225924378

Variant related genes	Relation type
ENSG00000226349	TF binding region
RNU6-1304P	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1461957	1.00[YRI][hapmap]
rs16845207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16845230	0.85[EUR][1000 genomes]
rs16845250	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2077840	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2234698	1.00[MEX][hapmap]
rs56052403	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56076632	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs74148699	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	60 gene(s)	inside rSNPs	diseases
5	nsv525391	chr1:225912620-225928538	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225912400-225924200	Weak transcription	Spleen	Spleen
2	chr1:225915200-225933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:225921400-225925600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:225921400-225934400	Weak transcription	Esophagus	oesophagus
5	chr1:225922200-225925800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:225922800-225924400	Enhancers	Stomach Mucosa	stomach
7	chr1:225922800-225924600	Enhancers	Placenta	Placenta
8	chr1:225922800-225925400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:225922800-225925600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:225922800-225925800	Enhancers	Liver	Liver
11	chr1:225922800-225925800	Enhancers	Fetal Lung	lung
12	chr1:225922800-225926000	Enhancers	Fetal Muscle Leg	muscle
13	chr1:225923000-225924200	Enhancers	Fetal Brain Female	brain
14	chr1:225923000-225924400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:225923000-225924400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr1:225923000-225924400	Enhancers	Psoas Muscle	Psoas
17	chr1:225923000-225924400	Enhancers	Right Ventricle	heart
18	chr1:225923000-225924600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:225923000-225924600	Enhancers	Gastric	stomach
20	chr1:225923000-225924600	Enhancers	Left Ventricle	heart
21	chr1:225923000-225924600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:225923000-225924800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:225923000-225925000	Enhancers	Fetal Stomach	stomach
24	chr1:225923000-225925200	Enhancers	Fetal Thymus	thymus
25	chr1:225923000-225925400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:225923000-225925600	Enhancers	Adipose Nuclei	Adipose
27	chr1:225923000-225925600	Flanking Active TSS	A549	lung
28	chr1:225923000-225925800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:225923000-225925800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:225923000-225925800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:225923000-225925800	Enhancers	Fetal Muscle Trunk	muscle
32	chr1:225923000-225925800	Enhancers	Right Atrium	heart
33	chr1:225923000-225925800	Flanking Active TSS	Hela-S3	cervix
34	chr1:225923000-225925800	Enhancers	NH-A	brain
35	chr1:225923000-225926000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:225923000-225926000	Enhancers	Fetal Heart	heart
37	chr1:225923200-225924400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:225923200-225924400	Enhancers	Brain Hippocampus Middle	brain
39	chr1:225923200-225924400	Enhancers	Fetal Kidney	kidney
40	chr1:225923200-225924600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:225923200-225924600	Enhancers	Brain Germinal Matrix	brain
42	chr1:225923200-225924600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:225923200-225925400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:225923200-225925600	Enhancers	HUVEC	blood vessel
45	chr1:225923400-225924200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:225923400-225924400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:225923400-225924400	Enhancers	Pancreas	Pancrea
48	chr1:225923400-225924400	Flanking Active TSS	HSMM	muscle
49	chr1:225923400-225924600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:225923400-225924600	Flanking Active TSS	HepG2	liver

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