Variant report

Variant	rs56741490
Chromosome Location	chr1:184723135-184723136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184723118..184724888-chr1:185124173..185126460,2	MCF-7	breast:
2	chr1:183996674..183999449-chr1:184721278..184723656,2	K562	blood:
3	chr1:184721288..184723463-chr1:185282046..185283828,2	K562	blood:
4	chr1:184721859..184724654-chr1:185126581..185128573,2	MCF-7	breast:
5	chr1:184722993..184726139-chr1:185013897..185016469,4	K562	blood:

Variant related genes	Relation type
ENSG00000121481	Chromatin interaction
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489697	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797985	0.87[EUR][1000 genomes]
rs10911628	0.87[EUR][1000 genomes]
rs10911637	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12060621	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12067111	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12079454	1.00[ASN][1000 genomes]
rs12094196	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12096214	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16823413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224092	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35779894	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41535944	0.88[AFR][1000 genomes]
rs55760657	0.94[AMR][1000 genomes]
rs55896922	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56384325	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58465130	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59085958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59347366	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59634722	0.94[AMR][1000 genomes]
rs59862212	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61022402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823870	1.00[AMR][1000 genomes]
rs61823871	1.00[AMR][1000 genomes]
rs61823873	1.00[AMR][1000 genomes]
rs61823876	0.94[AMR][1000 genomes]
rs61823879	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61823880	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681178	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3403637	chr1:184722554-184725102	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184677600-184723200	Weak transcription	Lung	lung
2	chr1:184717400-184723200	Weak transcription	Left Ventricle	heart
3	chr1:184721200-184723200	Weak transcription	Gastric	stomach
4	chr1:184721600-184723400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:184721800-184724600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:184721800-184725200	Active TSS	Psoas Muscle	Psoas
7	chr1:184721800-184725200	Active TSS	Stomach Mucosa	stomach
8	chr1:184722000-184723200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:184722000-184723200	Weak transcription	Esophagus	oesophagus
10	chr1:184722000-184723600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:184722000-184725000	Active TSS	GM12878-XiMat	blood
12	chr1:184722000-184725000	Active TSS	K562	blood
13	chr1:184722200-184723200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr1:184722200-184723200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:184722200-184723200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr1:184722200-184723200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:184722200-184723600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:184722200-184723600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:184722200-184723600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:184722200-184724600	Active TSS	Duodenum Mucosa	Duodenum
21	chr1:184722200-184724800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:184722200-184725200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:184722200-184725200	Active TSS	Fetal Stomach	stomach
24	chr1:184722200-184725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:184722400-184723200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:184722400-184723400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr1:184722400-184723400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:184722400-184724400	Active TSS	Fetal Thymus	thymus
29	chr1:184722400-184724800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:184722400-184725000	Active TSS	Fetal Intestine Large	intestine
31	chr1:184722400-184725000	Active TSS	Thymus	Thymus
32	chr1:184722600-184723200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:184722600-184723200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:184722600-184723200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:184722600-184723200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr1:184722600-184723200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:184722600-184723200	Flanking Active TSS	Fetal Brain Female	brain
38	chr1:184722600-184723200	Flanking Active TSS	NH-A	brain
39	chr1:184722600-184723200	Flanking Active TSS	Osteobl	bone
40	chr1:184722600-184723600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:184722600-184724000	Active TSS	Right Atrium	heart
42	chr1:184722600-184724400	Active TSS	HepG2	liver
43	chr1:184722600-184724600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:184722600-184724800	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:184722600-184724800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:184722600-184724800	Active TSS	HSMMtube	muscle
47	chr1:184722600-184725000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:184722600-184725000	Active TSS	Primary T cells fromperipheralblood	blood
49	chr1:184722600-184725000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:184722600-184725000	Active TSS	Brain Hippocampus Middle	brain

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