Variant report

Variant	rs1977877
Chromosome Location	chr20:25843216-25843217
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	TCF3	chr20:25842950-25843219	GM12878	blood:	n/a	n/a
2	FOSL2	chr20:25841795-25844457	HepG2	liver:	n/a	n/a
3	CEBPB	chr20:25843000-25843241	K562	blood:	n/a	n/a
4	PAX5	chr20:25842949-25843227	GM12878	blood:	n/a	n/a
5	RXRA	chr20:25842730-25844344	HepG2	liver:	n/a	n/a
6	POU2F2	chr20:25842920-25843237	GM12878	blood:	n/a	n/a
7	PAX5	chr20:25842877-25844432	GM12878	blood:	n/a	n/a
8	HEY1	chr20:25842932-25843238	K562	blood:	n/a	n/a
9	SIX5	chr20:25842982-25843279	K562	blood:	n/a	n/a

Variant related genes	Relation type
FAM182B	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13433200	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002942	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2380318	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2890395	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4121105	1.00[ASN][1000 genomes]
rs4813595	1.00[ASN][1000 genomes]
rs4815476	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815482	1.00[ASN][1000 genomes]
rs4815489	1.00[ASN][1000 genomes]
rs4815490	1.00[ASN][1000 genomes]
rs4815491	1.00[ASN][1000 genomes]
rs4815494	1.00[ASN][1000 genomes]
rs4815495	1.00[ASN][1000 genomes]
rs4815496	1.00[ASN][1000 genomes]
rs4815497	0.83[ASN][1000 genomes]
rs56040867	0.83[ASN][1000 genomes]
rs56059532	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59779961	1.00[ASN][1000 genomes]
rs60007971	1.00[ASN][1000 genomes]
rs6037252	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037270	1.00[ASN][1000 genomes]
rs6037305	1.00[ASN][1000 genomes]
rs6037306	1.00[ASN][1000 genomes]
rs6037307	1.00[ASN][1000 genomes]
rs6037311	1.00[ASN][1000 genomes]
rs6037313	1.00[ASN][1000 genomes]
rs6037314	1.00[ASN][1000 genomes]
rs6050932	1.00[ASN][1000 genomes]
rs6050939	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050941	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050948	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6050950	0.93[AFR][1000 genomes]
rs6050958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6051049	1.00[ASN][1000 genomes]
rs6051067	1.00[ASN][1000 genomes]
rs6051072	1.00[ASN][1000 genomes]
rs6051087	1.00[ASN][1000 genomes]
rs6107112	1.00[ASN][1000 genomes]
rs61091356	1.00[ASN][1000 genomes]
rs6115319	1.00[ASN][1000 genomes]
rs6115330	1.00[ASN][1000 genomes]
rs6115340	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115343	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115347	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115350	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115351	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115353	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115355	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7267539	1.00[ASN][1000 genomes]
rs7274331	1.00[ASN][1000 genomes]
rs7345455	1.00[ASN][1000 genomes]
rs9653636	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
2	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv979422	chr20:25732656-25867609	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv10664	chr20:25767042-25849064	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv585749	chr20:25767347-25856929	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv585752	chr20:25786189-25864851	ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv585753	chr20:25786189-25892571	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv585754	chr20:25786301-25864851	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv585755	chr20:25786301-25871801	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv585756	chr20:25786301-25948094	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv585757	chr20:25786301-25948327	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv585758	chr20:25786984-25951658	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv585759	chr20:25787096-25948327	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1059041	chr20:25832105-26007269	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1060065	chr20:25832105-26305567	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
17	nsv9795	chr20:25832369-25851689	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv979451	chr20:25836169-25856112	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv3502991	chr20:25837879-25847973	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv3502992	chr20:25837879-25847973	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	esv3429566	chr20:25838143-25848095	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25840000-25845000	Flanking Bivalent TSS/Enh	HepG2	liver
2	chr20:25840400-25844400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr20:25840400-25844400	Active TSS	Brain Angular Gyrus	brain
4	chr20:25840400-25844800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr20:25841600-25844800	Active TSS	Hela-S3	cervix
6	chr20:25841600-25845000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:25841800-25843600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr20:25841800-25843800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:25841800-25844000	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr20:25841800-25844600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr20:25841800-25847200	Enhancers	Spleen	Spleen
12	chr20:25842000-25844200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:25842000-25844400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:25842000-25844400	Active TSS	Psoas Muscle	Psoas
15	chr20:25842000-25844600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr20:25842000-25844600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr20:25842200-25843600	Bivalent Enhancer	Fetal Thymus	thymus
18	chr20:25842200-25844400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:25842200-25844600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr20:25842200-25844800	Flanking Active TSS	Dnd41	blood
21	chr20:25842400-25843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:25842400-25843800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
23	chr20:25842400-25844000	Enhancers	Lung	lung
24	chr20:25842600-25843400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr20:25842600-25843400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:25842600-25843400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
27	chr20:25842600-25843600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr20:25842600-25843600	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr20:25842600-25843600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr20:25842600-25843600	Enhancers	Pancreas	Pancrea
31	chr20:25842600-25843800	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr20:25842600-25843800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr20:25842600-25843800	Flanking Active TSS	Right Ventricle	heart
34	chr20:25842800-25843400	Bivalent Enhancer	Primary B cells from cord blood	blood
35	chr20:25842800-25843400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr20:25842800-25843400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr20:25842800-25843400	Enhancers	K562	blood
38	chr20:25842800-25843600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
39	chr20:25842800-25843600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
40	chr20:25842800-25843600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr20:25842800-25843600	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr20:25842800-25843600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr20:25842800-25843600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr20:25842800-25843600	Enhancers	Ovary	ovary
45	chr20:25842800-25843600	Enhancers	HMEC	breast
46	chr20:25842800-25843800	Bivalent Enhancer	Fetal Lung	lung
47	chr20:25842800-25843800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr20:25842800-25844000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr20:25843000-25843400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr20:25843000-25843400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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