Variant report

Variant	rs6057406
Chromosome Location	chr20:29641168-29641169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:29640916..29641744-chr4:190895394..190895909,2	MCF-7	breast:
2	chr20:29637719..29639568-chr20:29640126..29641910,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238151	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs34988612	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4892328	0.82[ASN][1000 genomes]
rs6057191	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6057373	0.88[ASN][1000 genomes]
rs6057378	0.90[ASN][1000 genomes]
rs6087167	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6087264	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6087306	0.82[ASN][1000 genomes]
rs6118923	0.94[ASN][1000 genomes]
rs6119084	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6119089	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6119118	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6141218	0.98[ASN][1000 genomes]
rs8117830	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758518	chr20:29419570-29653908	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2758791	chr20:29419570-29653908	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428028	chr20:29419570-29653908	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv428376	chr20:29419570-29653908	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1058387	chr20:29479828-29651199	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1067193	chr20:29525410-29651199	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv11674	chr20:29528011-29653880	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv965870	chr20:29570138-29652376	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv15335	chr20:29580700-29653880	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv585870	chr20:29603773-29648195	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv585871	chr20:29612406-29648195	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv585872	chr20:29612406-29648263	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv585873	chr20:29616742-29651821	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv821487	chr20:29629343-29652652	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv828711	chr20:29629343-29652652	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv585874	chr20:29633277-29651821	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv7214	chr20:29638542-29641660	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv436321	chr20:29638637-29645554	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3420645	chr20:29638675-29641488	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv3419758	chr20:29638695-29641497	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv3446706	chr20:29638696-29641520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	esv3485532	chr20:29638699-29641449	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	esv3454242	chr20:29638730-29641427	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	esv3454243	chr20:29638730-29641427	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	esv3404333	chr20:29638731-29641480	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	esv3485533	chr20:29638754-29641449	ZNF genes & repeats Strong transcription Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	esv3485530	chr20:29638754-29641456	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:29638600-29641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:29638600-29641400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:29638600-29641400	Weak transcription	Left Ventricle	heart
4	chr20:29638600-29641400	Weak transcription	Right Ventricle	heart
5	chr20:29638800-29641200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:29638800-29641200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr20:29638800-29641400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr20:29638800-29641400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:29638800-29641400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:29638800-29641400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:29638800-29641400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr20:29638800-29641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr20:29638800-29641400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:29638800-29641400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr20:29638800-29641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:29638800-29641400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:29638800-29641400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr20:29638800-29641400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr20:29638800-29641400	Weak transcription	Adipose Nuclei	Adipose
20	chr20:29638800-29641400	Weak transcription	Brain Angular Gyrus	brain
21	chr20:29638800-29641400	Weak transcription	Brain Anterior Caudate	brain
22	chr20:29638800-29641400	Weak transcription	Brain Hippocampus Middle	brain
23	chr20:29638800-29641400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr20:29638800-29641400	Weak transcription	Colon Smooth Muscle	Colon
25	chr20:29638800-29641400	Weak transcription	Fetal Heart	heart
26	chr20:29638800-29641400	Weak transcription	Fetal Kidney	kidney
27	chr20:29638800-29641400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr20:29638800-29641400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr20:29638800-29641400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr20:29638800-29641400	Weak transcription	A549	lung
31	chr20:29638800-29641400	Weak transcription	GM12878-XiMat	blood
32	chr20:29638800-29641400	Weak transcription	HSMM	muscle
33	chr20:29638800-29641400	Weak transcription	HUVEC	blood vessel
34	chr20:29638800-29641400	Weak transcription	K562	blood
35	chr20:29638800-29641400	Weak transcription	NH-A	brain
36	chr20:29638800-29641400	Weak transcription	NHDF-Ad	bronchial
37	chr20:29638800-29641600	Weak transcription	Brain Substantia Nigra	brain
38	chr20:29638800-29641800	Weak transcription	Placenta	Placenta
39	chr20:29639000-29641200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr20:29639000-29641200	Weak transcription	Primary T cells from cord blood	blood
41	chr20:29639000-29641200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr20:29639000-29641200	Weak transcription	Fetal Lung	lung
43	chr20:29639000-29641400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:29639000-29641400	Weak transcription	Primary B cells from cord blood	blood
45	chr20:29639000-29641400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr20:29639000-29641400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr20:29639000-29641400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr20:29639000-29641400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr20:29639000-29641400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:29639000-29641400	Weak transcription	Liver	Liver

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