Variant report

Variant	rs16862745
Chromosome Location	chr1:169860199-169860200
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	GATA3	chr1:169859983-169860993	T-47D	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861
2	KAP1	chr1:169859735-169860669	HEK293	kidney:	n/a	n/a
3	KAP1	chr1:169859874-169860453	U2OS	brain:	n/a	n/a
4	POLR2A	chr1:169860176-169860946	GM12891	blood:	n/a	n/a
5	SPI1	chr1:169860179-169860574	GM12891	blood:	n/a	n/a
6	WRNIP1	chr1:169859975-169860710	GM12878	blood:	n/a	n/a
7	EBF1	chr1:169860194-169861050	GM12878	blood:	n/a	chr1:169860843-169860854
8	RUNX3	chr1:169860086-169860885	GM12878	blood:	n/a	chr1:169860718-169860733
9	POLR2A	chr1:169860178-169860654	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:169860074-169860811	GM12892	blood:	n/a	n/a
11	MTA3	chr1:169859892-169861058	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:169859946-169860971	GM12891	blood:	n/a	n/a
13	SIX5	chr1:169860070-169860436	GM12878	blood:	n/a	n/a
14	SPI1	chr1:169860111-169860503	GM12891	blood:	n/a	n/a
15	NFIC	chr1:169860085-169860828	GM12878	blood:	n/a	n/a
16	RUNX3	chr1:169860107-169860752	GM12878	blood:	n/a	chr1:169860718-169860733
17	SP1	chr1:169860153-169860934	HCT-116	colon:	n/a	n/a
18	MTA3	chr1:169860053-169860783	GM12878	blood:	n/a	n/a
19	SPI1	chr1:169860193-169860480	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:169860190-169860846	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169858457..169860973-chr1:169907396..169909921,2	MCF-7	breast:
2	chr1:169704931..169706505-chr1:169859799..169862220,2	K562	blood:
3	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
4	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10489172	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1062976	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800468	1.00[ASN][1000 genomes]
rs10919250	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919252	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs10919255	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919256	0.81[AMR][1000 genomes]
rs10919259	0.81[AMR][1000 genomes]
rs10919267	0.94[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919283	0.82[YRI][hapmap]
rs11576078	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589247	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064636	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084893	1.00[ASN][1000 genomes]
rs12089057	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405525	0.81[AMR][1000 genomes]
rs12760399	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330377	0.88[YRI][hapmap]
rs1541160	0.86[YRI][hapmap]
rs17529513	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603022	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050628	0.82[YRI][hapmap]
rs2065950	0.88[YRI][hapmap]
rs2272918	0.81[AMR][1000 genomes]
rs2474708	0.88[YRI][hapmap]
rs35296671	0.82[EUR][1000 genomes]
rs476269	0.80[YRI][hapmap]
rs4987280	1.00[ASN][1000 genomes]
rs516793	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs522444	0.88[YRI][hapmap]
rs527261	0.86[YRI][hapmap]
rs541896	0.88[YRI][hapmap]
rs546894	0.86[YRI][hapmap]
rs549002	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs571398	0.83[YRI][hapmap]
rs614044	0.88[YRI][hapmap]
rs621437	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs628436	0.88[YRI][hapmap]
rs6427230	0.81[YRI][hapmap]
rs6427232	0.93[YRI][hapmap]
rs648576	0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs659476	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs6668310	0.86[YRI][hapmap]
rs6678351	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694304	0.88[YRI][hapmap]
rs6694855	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026213	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026223	0.88[AMR][1000 genomes]
rs73026243	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026245	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539241	0.88[YRI][hapmap]
rs973015	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS 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 target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169833800-169860200	Weak transcription	HMEC	breast
3	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
5	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
8	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
9	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
12	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
15	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle
16	chr1:169855200-169861200	Weak transcription	HSMM	muscle
17	chr1:169855400-169861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:169855800-169860200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:169856000-169861400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:169856000-169861400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:169856200-169861400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:169857400-169860400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:169857400-169861400	Weak transcription	Fetal Brain Female	brain
24	chr1:169857600-169860800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:169857600-169861200	Weak transcription	Hela-S3	cervix
26	chr1:169857800-169860200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:169857800-169860200	Weak transcription	NH-A	brain
28	chr1:169857800-169860400	Weak transcription	Fetal Kidney	kidney
29	chr1:169858000-169860400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:169858000-169860400	Weak transcription	HUVEC	blood vessel
31	chr1:169858000-169860600	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:169858000-169860600	Weak transcription	NHLF	lung
33	chr1:169858000-169860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:169858000-169860800	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:169858000-169861400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:169858000-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:169858000-169861400	Weak transcription	Fetal Brain Male	brain
38	chr1:169858000-169861400	Weak transcription	K562	blood
39	chr1:169858200-169860200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:169858200-169860400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:169858200-169861200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:169858200-169861200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:169858200-169861400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:169858200-169861400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:169858600-169860200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:169858800-169861200	Enhancers	Liver	Liver
47	chr1:169858800-169861600	Enhancers	Small Intestine	intestine
48	chr1:169859000-169860200	Enhancers	Pancreas	Pancrea
49	chr1:169859000-169860200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr1:169859000-169860600	Enhancers	Esophagus	oesophagus

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