Variant report

Variant	rs6040009
Chromosome Location	chr20:1105144-1105145
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	chr20:1098147..1101828-chr20:1104480..1108337,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11908561	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1803415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883522	0.86[ASN][1000 genomes]
rs2072961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072962	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072963	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072964	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179449	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179450	0.86[ASN][1000 genomes]
rs2235587	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2268065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284375	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787572	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142353	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289256	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040066	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040108	0.86[ASN][1000 genomes]
rs6133957	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6133961	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6133989	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100200-1105800	Weak transcription	Aorta	Aorta
2	chr20:1100200-1106200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:1100400-1105800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:1100400-1106200	Weak transcription	HSMMtube	muscle
5	chr20:1100400-1115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:1100400-1132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr20:1100600-1105200	Enhancers	Psoas Muscle	Psoas
9	chr20:1100600-1105800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:1100600-1105800	Weak transcription	Esophagus	oesophagus
11	chr20:1100600-1106000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:1100800-1106400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr20:1100800-1122200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr20:1101000-1105800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:1101000-1105800	Weak transcription	Fetal Kidney	kidney
16	chr20:1101200-1105800	Weak transcription	Colonic Mucosa	Colon
17	chr20:1101200-1105800	Weak transcription	NH-A	brain
18	chr20:1101400-1105400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr20:1101600-1105200	Enhancers	Brain Cingulate Gyrus	brain
20	chr20:1101600-1105800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:1101600-1105800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr20:1101600-1105800	Weak transcription	Spleen	Spleen
23	chr20:1101800-1105600	Weak transcription	HSMM	muscle
24	chr20:1101800-1105800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:1101800-1111600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:1102200-1105200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr20:1102200-1105400	Weak transcription	Fetal Intestine Large	intestine
28	chr20:1102200-1105600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr20:1102200-1105800	Weak transcription	Fetal Brain Female	brain
30	chr20:1102200-1106000	Weak transcription	Gastric	stomach
31	chr20:1102200-1106200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr20:1102200-1107600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr20:1102200-1128600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr20:1102600-1105800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr20:1102600-1111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:1102800-1113800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr20:1103200-1105800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr20:1103400-1105400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr20:1103400-1105400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr20:1103400-1105800	Weak transcription	Brain Angular Gyrus	brain
41	chr20:1103400-1105800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr20:1103400-1106000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr20:1103400-1106200	Weak transcription	Pancreas	Pancrea
44	chr20:1103400-1106200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr20:1103600-1105200	Enhancers	Brain Anterior Caudate	brain
46	chr20:1103600-1105400	Weak transcription	Brain Germinal Matrix	brain
47	chr20:1103600-1105800	Weak transcription	Ovary	ovary
48	chr20:1103600-1105800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr20:1103600-1105800	Weak transcription	Thymus	Thymus
50	chr20:1103600-1106000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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