Variant report

Variant	rs56400900
Chromosome Location	chr5:43556386-43556387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43119888..43121712-chr5:43555739..43557363,2	K562	blood:
2	chr5:43555487..43559521-chr5:43598404..43605405,16	K562	blood:
3	chr5:43513317..43519979-chr5:43552519..43558793,19	K562	blood:
4	chr5:43512478..43519226-chr5:43552704..43558861,10	MCF-7	breast:
5	chr5:43120689..43121650-chr5:43556319..43557143,3	Hela-S3	cervix:
6	chr5:43482505..43485566-chr5:43554663..43558409,7	MCF-7	breast:
7	chr5:43121048..43123106-chr5:43555521..43557723,3	MCF-7	breast:
8	chr5:43513876..43516684-chr5:43553510..43558785,6	MCF-7	breast:
9	chr3:49058506..49059032-chr5:43556383..43557190,2	Hela-S3	cervix:
10	chr1:161735480..161736094-chr5:43556295..43557137,2	Hela-S3	cervix:
11	chr5:43555203..43556754-chr5:43587792..43589517,2	MCF-7	breast:
12	chr5:43481238..43485996-chr5:43553681..43560344,12	K562	blood:
13	chr5:43552832..43560830-chr5:43598877..43605844,26	MCF-7	breast:
14	chr5:43505282..43507808-chr5:43556089..43557593,2	K562	blood:
15	chr5:43556013..43559876-chr5:43586120..43588801,3	K562	blood:
16	chr5:43479992..43486255-chr5:43553479..43560182,13	MCF-7	breast:
17	chr5:43063931..43068016-chr5:43554200..43557480,3	K562	blood:
18	chr5:43505801..43507815-chr5:43555939..43557727,2	MCF-7	breast:
19	chr5:43555382..43559666-chr5:43598979..43604929,17	K562	blood:
20	chr5:43513317..43518816-chr5:43554982..43559074,7	K562	blood:
21	chr5:43554854..43559895-chr5:43599481..43606699,15	MCF-7	breast:
22	chr5:43556054..43556894-chrX:154255366..154256157,2	Hela-S3	cervix:
23	chr5:43555615..43556531-chr6:27100554..27101250,2	Hela-S3	cervix:
24	chr5:43119211..43122555-chr5:43554907..43559759,4	K562	blood:
25	chr5:43481891..43486310-chr5:43553986..43559337,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177738	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000165775	Chromatin interaction
ENSG00000249286	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000248092	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10036954	0.83[EUR][1000 genomes]
rs10038608	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10042992	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10043934	0.82[EUR][1000 genomes]
rs10045455	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10057103	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10058558	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10061165	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10065863	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10447144	0.83[EUR][1000 genomes]
rs10462051	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10473311	0.82[EUR][1000 genomes]
rs1072745	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1072746	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10941640	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12332560	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12651879	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12652547	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12659369	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12697452	0.82[ASN][1000 genomes]
rs13185343	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13189004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13360902	0.99[ASN][1000 genomes]
rs1428640	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2013173	0.83[EUR][1000 genomes]
rs2132000	0.81[EUR][1000 genomes]
rs2172763	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34007811	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35710460	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35881272	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36013953	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776423	0.83[EUR][1000 genomes]
rs3806870	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073848	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073850	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4073851	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4242099	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4308491	0.85[EUR][1000 genomes]
rs4331909	0.89[EUR][1000 genomes]
rs4367306	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4415083	0.85[EUR][1000 genomes]
rs4467713	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4513704	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4541663	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4576155	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4610465	0.96[ASN][1000 genomes]
rs4866746	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4866752	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4866833	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55641556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57547662	0.82[EUR][1000 genomes]
rs57597020	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6451692	0.81[EUR][1000 genomes]
rs6451695	0.82[EUR][1000 genomes]
rs6451696	0.82[EUR][1000 genomes]
rs6451698	0.82[EUR][1000 genomes]
rs6451703	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6451704	0.83[EUR][1000 genomes]
rs6451706	0.86[EUR][1000 genomes]
rs6451712	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451718	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs67466542	0.83[EUR][1000 genomes]
rs67581152	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6861704	0.85[EUR][1000 genomes]
rs6862102	0.82[EUR][1000 genomes]
rs6865217	0.85[EUR][1000 genomes]
rs6870018	0.81[EUR][1000 genomes]
rs6870783	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6883661	0.83[EUR][1000 genomes]
rs7701429	0.84[ASN][1000 genomes]
rs7707976	0.80[EUR][1000 genomes]
rs7708072	0.85[ASN][1000 genomes]
rs7708443	0.80[EUR][1000 genomes]
rs7710125	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7717636	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7724571	0.81[EUR][1000 genomes]
rs7731091	0.82[EUR][1000 genomes]
rs7734393	0.89[EUR][1000 genomes]
rs7735243	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7737793	0.96[ASN][1000 genomes]
rs9292883	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9687341	0.84[EUR][1000 genomes]
rs9885467	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription 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	220 gene(s)	inside rSNPs	diseases
3	esv1835057	chr5:43515280-43557405	Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	esv12689	chr5:43556383-43557492	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43554000-43557800	Active TSS	Right Ventricle	heart
2	chr5:43554800-43557400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:43554800-43557400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:43554800-43557400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:43554800-43557800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:43554800-43558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:43555000-43556400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr5:43555000-43556400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:43555000-43557400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:43555000-43557400	Active TSS	NHLF	lung
11	chr5:43555000-43557600	Active TSS	HSMMtube	muscle
12	chr5:43555000-43557800	Active TSS	Psoas Muscle	Psoas
13	chr5:43555200-43556400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:43555200-43556400	Active TSS	Right Atrium	heart
15	chr5:43555200-43556400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr5:43555200-43558000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:43555200-43558000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:43555200-43558000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:43555400-43556400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:43555400-43557400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:43555400-43557400	Active TSS	HMEC	breast
22	chr5:43555400-43557400	Active TSS	HSMM	muscle
23	chr5:43555400-43557400	Active TSS	NH-A	brain
24	chr5:43555400-43557800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:43555400-43558000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr5:43555400-43558000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr5:43555400-43558000	Active TSS	Fetal Intestine Large	intestine
28	chr5:43555600-43556400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr5:43555600-43556400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:43555600-43556400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr5:43555600-43556400	Flanking Active TSS	Liver	Liver
32	chr5:43555600-43556400	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr5:43555600-43556800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr5:43555600-43557600	Active TSS	Fetal Stomach	stomach
35	chr5:43555600-43557600	Active TSS	Fetal Thymus	thymus
36	chr5:43555600-43557600	Active TSS	GM12878-XiMat	blood
37	chr5:43555600-43557600	Active TSS	K562	blood
38	chr5:43555600-43558000	Active TSS	H9 Cell Line	embryonic stem cell
39	chr5:43555600-43558000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:43555600-43558000	Active TSS	Fetal Brain Female	brain
41	chr5:43555800-43556400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr5:43555800-43556400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr5:43555800-43556400	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr5:43555800-43556400	Active TSS	Brain Germinal Matrix	brain
45	chr5:43555800-43556400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr5:43555800-43556600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr5:43555800-43556600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr5:43555800-43556600	Active TSS	Fetal Heart	heart
49	chr5:43555800-43557400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr5:43555800-43557400	Active TSS	Cortex derived primary cultured neurospheres	brain

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