Variant report

Variant	rs56798454
Chromosome Location	chr15:56515548-56515549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56514134..56517478-chr15:56536032..56539404,3	K562	blood:
2	chr15:56500425..56503148-chr15:56514379..56516558,2	K562	blood:
3	chr15:56511715..56515864-chr15:56532488..56536636,4	MCF-7	breast:
4	chr15:56512622..56516382-chr15:56518362..56521999,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFX7-1	chr15:56514392-56516403	ucscGeneNc_uc002afb_1

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10444835	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071244	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071248	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071251	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438262	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438452	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438525	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438606	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438670	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439033	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440495	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440898	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443028	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443486	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976721	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976722	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976737	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976776	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976787	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976793	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976808	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16976820	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976824	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718927	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28895323	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310793	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180561	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181011	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2760380	chr15:56510123-56529955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 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	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:56508000-56534400	Weak transcription	Fetal Heart	heart
3	chr15:56508200-56524000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:56508400-56523000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:56509000-56533600	Weak transcription	Osteobl	bone
6	chr15:56509800-56522400	Weak transcription	Fetal Brain Male	brain
7	chr15:56510200-56523200	Weak transcription	NH-A	brain
8	chr15:56510600-56518000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr15:56510600-56528600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:56510800-56517800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:56512200-56519600	Weak transcription	HSMM	muscle
12	chr15:56513800-56515600	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr15:56513800-56517000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr15:56513800-56523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:56513800-56530200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr15:56514000-56515800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:56514000-56515800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr15:56514000-56535000	Weak transcription	Pancreas	Pancrea
19	chr15:56514200-56515800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
20	chr15:56514400-56515600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:56514400-56515600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:56514400-56515800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr15:56514400-56515800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr15:56514400-56515800	ZNF genes & repeats	HepG2	liver
25	chr15:56514400-56515800	ZNF genes & repeats	NHEK	skin
26	chr15:56514400-56516000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr15:56514400-56516000	ZNF genes & repeats	A549	lung
28	chr15:56514600-56515800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:56514600-56515800	ZNF genes & repeats	Liver	Liver
30	chr15:56514600-56516200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:56514600-56532400	Weak transcription	HSMMtube	muscle
32	chr15:56514800-56515600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr15:56514800-56515600	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr15:56514800-56516000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:56514800-56516200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:56514800-56516400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:56514800-56520400	Weak transcription	Fetal Kidney	kidney
38	chr15:56514800-56534800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:56515000-56515800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:56515000-56515800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:56515000-56518400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:56515200-56515600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr15:56515200-56515600	ZNF genes & repeats	Ovary	ovary
44	chr15:56515200-56515600	ZNF genes & repeats	Thymus	Thymus
45	chr15:56515200-56515800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:56515200-56515800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr15:56515200-56515800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:56515200-56515800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:56515200-56515800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:56515200-56515800	ZNF genes & repeats	Fetal Intestine Small	intestine

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