Variant report

Variant	rs10016977
Chromosome Location	chr4:56271942-56271943
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56261229..56262985-chr4:56271789..56273503,2	MCF-7	breast:
2	chr4:56266067..56267699-chr4:56271922..56273908,2	MCF-7	breast:
3	chr4:56269662..56272449-chr4:56297179..56299575,2	K562	blood:
4	chr4:56269741..56272367-chr4:56273938..56276057,3	MCF-7	breast:
5	chr4:56211424..56214450-chr4:56271067..56273644,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10010919	0.85[AFR][1000 genomes]
rs10026202	0.80[AFR][1000 genomes]
rs10031345	0.80[AFR][1000 genomes]
rs10155441	0.85[AFR][1000 genomes]
rs11133401	0.81[AFR][1000 genomes]
rs11727642	0.80[AFR][1000 genomes]
rs28369166	0.85[AFR][1000 genomes]
rs28375674	0.81[AFR][1000 genomes]
rs28376882	0.91[AFR][1000 genomes]
rs28391333	0.80[AFR][1000 genomes]
rs28401668	0.90[AFR][1000 genomes]
rs28418730	0.85[AFR][1000 genomes]
rs28456193	0.81[AFR][1000 genomes]
rs28547142	0.81[AFR][1000 genomes]
rs28548946	0.81[AFR][1000 genomes]
rs28588862	0.80[AFR][1000 genomes]
rs28590090	0.81[AFR][1000 genomes]
rs28606621	1.00[AFR][1000 genomes]
rs28683692	0.81[AFR][1000 genomes]
rs28712413	1.00[AFR][1000 genomes]
rs34401111	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264200-56273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:56265000-56273200	Weak transcription	Gastric	stomach
5	chr4:56265400-56273400	Weak transcription	Aorta	Aorta
6	chr4:56265600-56272000	Weak transcription	Esophagus	oesophagus
7	chr4:56265600-56272200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:56265600-56273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:56265600-56273800	Weak transcription	Stomach Mucosa	stomach
10	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
13	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
14	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:56265800-56274400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:56265800-56275200	Weak transcription	Fetal Heart	heart
18	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:56266000-56272000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:56266200-56275600	Weak transcription	Right Ventricle	heart
22	chr4:56266400-56272800	Weak transcription	Pancreas	Pancrea
23	chr4:56266600-56274200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:56267400-56272000	Weak transcription	Brain Angular Gyrus	brain
25	chr4:56267400-56274200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:56267400-56275200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:56267400-56280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:56267400-56282800	Weak transcription	Small Intestine	intestine
29	chr4:56267400-56283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:56267600-56275800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:56267600-56280800	Weak transcription	A549	lung
32	chr4:56267800-56273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:56268800-56272800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:56269000-56272400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:56269000-56273200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:56269000-56273600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:56269000-56274400	Strong transcription	HSMM	muscle
39	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:56269200-56273000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:56269200-56273400	Strong transcription	Osteobl	bone
42	chr4:56269200-56273800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr4:56269200-56274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:56269200-56274000	Strong transcription	NH-A	brain
45	chr4:56269200-56274000	Strong transcription	NHDF-Ad	bronchial
46	chr4:56269200-56274200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:56269200-56274200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:56269200-56274200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:56269200-56274200	Strong transcription	Fetal Intestine Large	intestine
50	chr4:56269200-56274600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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