Variant report

Variant	rs6037138
Chromosome Location	chr20:25530353-25530354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25527993..25531935-chr20:25532103..25536605,5	MCF-7	breast:
2	chr20:25528846..25530545-chr20:25675898..25678279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130684	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1539594	1.00[EUR][1000 genomes]
rs16987981	1.00[EUR][1000 genomes]
rs16987989	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16988008	1.00[EUR][1000 genomes]
rs16988024	1.00[EUR][1000 genomes]
rs242123	0.86[AFR][1000 genomes]
rs41308056	1.00[EUR][1000 genomes]
rs6037154	0.86[AFR][1000 genomes]
rs6050672	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6050691	0.86[AFR][1000 genomes]
rs6050768	1.00[CEU][hapmap]
rs7266033	1.00[CEU][hapmap]
rs73111297	0.86[AFR][1000 genomes]
rs73111300	0.86[AFR][1000 genomes]
rs73113113	0.86[AFR][1000 genomes]
rs73337350	0.83[EUR][1000 genomes]
rs73341353	0.83[EUR][1000 genomes]
rs73345239	0.83[EUR][1000 genomes]
rs8123947	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer 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	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
18	esv18920	chr20:25529198-25530408	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:25520000-25532000	Weak transcription	Dnd41	blood
4	chr20:25521200-25530600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr20:25521400-25532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:25521400-25534200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
8	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:25524800-25531600	Enhancers	Fetal Lung	lung
10	chr20:25525000-25535400	Enhancers	Fetal Heart	heart
11	chr20:25526200-25534400	Weak transcription	Brain Substantia Nigra	brain
12	chr20:25526400-25543600	Weak transcription	Fetal Brain Female	brain
13	chr20:25526600-25530400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr20:25526600-25534200	Weak transcription	Brain Hippocampus Middle	brain
15	chr20:25526600-25540200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr20:25527800-25530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr20:25527800-25532200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr20:25528000-25530400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr20:25528200-25531200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr20:25528400-25530400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr20:25528600-25530400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:25528600-25530400	Enhancers	Pancreas	Pancrea
23	chr20:25528600-25530400	Genic enhancers	HepG2	liver
24	chr20:25528600-25531200	Enhancers	Esophagus	oesophagus
25	chr20:25528800-25531000	Enhancers	Gastric	stomach
26	chr20:25528800-25531000	Enhancers	Spleen	Spleen
27	chr20:25528800-25531200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:25529000-25531000	Enhancers	Lung	lung
29	chr20:25529000-25531200	Enhancers	Stomach Mucosa	stomach
30	chr20:25529000-25532600	Enhancers	Fetal Intestine Large	intestine
31	chr20:25529000-25535600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25529200-25530400	Enhancers	Placenta	Placenta
33	chr20:25529200-25531000	Enhancers	Hela-S3	cervix
34	chr20:25529200-25531200	Enhancers	Ovary	ovary
35	chr20:25529200-25531400	Enhancers	Fetal Intestine Small	intestine
36	chr20:25529400-25531200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr20:25529400-25531400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:25529600-25533800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr20:25529600-25534200	Weak transcription	Thymus	Thymus
40	chr20:25529800-25530400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr20:25529800-25530800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:25529800-25530800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr20:25529800-25530800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr20:25529800-25531000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:25529800-25531000	Enhancers	NHLF	lung
46	chr20:25529800-25531200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr20:25529800-25531200	Enhancers	Fetal Muscle Trunk	muscle
48	chr20:25529800-25531200	Enhancers	Fetal Muscle Leg	muscle
49	chr20:25529800-25533000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr20:25530000-25530400	Flanking Active TSS	Adipose Nuclei	Adipose

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