Variant report

Variant	rs6050941
Chromosome Location	chr20:25839669-25839670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25604447..25606097-chr20:25837225..25840203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170191	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs13433200	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977877	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002942	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2380318	0.84[EUR][1000 genomes]
rs2890395	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4121105	1.00[ASN][1000 genomes]
rs4813595	1.00[ASN][1000 genomes]
rs4815476	0.85[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59779961	1.00[ASN][1000 genomes]
rs60007971	1.00[ASN][1000 genomes]
rs6037230	0.80[GIH][hapmap];1.00[MEX][hapmap]
rs6037252	0.86[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	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050958	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050997	1.00[CHB][hapmap]
rs6051049	1.00[ASN][1000 genomes]
rs6051067	1.00[ASN][1000 genomes]
rs6051072	1.00[ASN][1000 genomes]
rs6051087	1.00[ASN][1000 genomes]
rs6107062	1.00[CHB][hapmap]
rs6107064	1.00[CHB][hapmap]
rs6107112	1.00[ASN][1000 genomes]
rs61091356	1.00[ASN][1000 genomes]
rs6115248	1.00[CHD][hapmap]
rs6115319	1.00[ASN][1000 genomes]
rs6115330	1.00[ASN][1000 genomes]
rs6115340	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115343	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115347	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115350	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115351	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115353	0.84[EUR][1000 genomes]
rs6115355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115405	1.00[CHB][hapmap]
rs6115429	1.00[CHB][hapmap]
rs6515674	0.94[MEX][hapmap]
rs7267539	1.00[ASN][1000 genomes]
rs7268237	1.00[CHB][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap]
rs7274331	1.00[ASN][1000 genomes]
rs7345455	1.00[ASN][1000 genomes]
rs9653636	0.81[EUR][1000 genomes];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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25835000-25840200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr20:25837800-25840200	Active TSS	Brain Germinal Matrix	brain
3	chr20:25837800-25840200	Active TSS	Fetal Brain Female	brain
4	chr20:25838200-25839800	Active TSS	Brain Angular Gyrus	brain
5	chr20:25838400-25840400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr20:25838400-25842000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr20:25838400-25842200	ZNF genes & repeats	Dnd41	blood
8	chr20:25838600-25839800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr20:25838600-25840000	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr20:25838600-25842000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr20:25838800-25839800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr20:25839000-25840000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr20:25839000-25840600	Bivalent Enhancer	Fetal Brain Male	brain
14	chr20:25839200-25839800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr20:25839200-25839800	Flanking Active TSS	Brain Substantia Nigra	brain
16	chr20:25839200-25840200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:25839200-25840400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr20:25839200-25842000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr20:25839400-25839800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
20	chr20:25839400-25839800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr20:25839400-25840000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr20:25839400-25840200	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr20:25839400-25840200	Weak transcription	Left Ventricle	heart
24	chr20:25839400-25840200	Enhancers	Right Ventricle	heart
25	chr20:25839400-25840400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr20:25839400-25840400	Weak transcription	Ovary	ovary
27	chr20:25839400-25840400	Weak transcription	Psoas Muscle	Psoas
28	chr20:25839400-25840400	Weak transcription	Right Atrium	heart
29	chr20:25839400-25840400	Weak transcription	A549	lung
30	chr20:25839400-25841000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:25839400-25841400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr20:25839400-25842000	Bivalent Enhancer	Placenta	Placenta
33	chr20:25839400-25842600	Enhancers	Fetal Heart	heart
34	chr20:25839600-25839800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr20:25839600-25839800	Flanking Bivalent TSS/Enh	HepG2	liver
36	chr20:25839600-25840000	Weak transcription	Liver	Liver
37	chr20:25839600-25840000	Active TSS	Brain Cingulate Gyrus	brain
38	chr20:25839600-25840000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr20:25839600-25840000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr20:25839600-25840000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr20:25839600-25840000	Weak transcription	GM12878-XiMat	blood
42	chr20:25839600-25840000	Weak transcription	K562	blood
43	chr20:25839600-25840200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:25839600-25840200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr20:25839600-25840200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr20:25839600-25840200	Weak transcription	Pancreas	Pancrea
47	chr20:25839600-25840200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
48	chr20:25839600-25840400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
49	chr20:25839600-25840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:25839600-25840400	Bivalent Enhancer	Adipose Nuclei	Adipose

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