Variant report

Variant	rs56270003
Chromosome Location	chr4:7805994-7805995
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:7804029..7806912-chr4:7851204..7853700,2	MCF-7	breast:
2	chr4:7804713..7806247-chr4:7939917..7942517,2	MCF-7	breast:
3	chr4:7805561..7806399-chr4:7988705..7989541,5	MCF-7	breast:
4	chr4:7805604..7807190-chr4:7845615..7846654,7	MCF-7	breast:
5	chr4:7805902..7806736-chr4:7939845..7940494,2	MCF-7	breast:
6	chr4:7805394..7806236-chr4:7877431..7878287,4	MCF-7	breast:
7	chr4:7805419..7806405-chr4:7988814..7989339,2	K562	blood:
8	chr4:7804324..7807098-chr4:7992889..7994621,2	MCF-7	breast:
9	chr4:7805566..7806506-chr4:7851979..7852511,2	K562	blood:
10	chr4:7805249..7806076-chr4:7845775..7846418,2	MCF-7	breast:
11	chr4:7805890..7806402-chr4:7930617..7931480,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11721583	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11721609	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11724632	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11728778	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11729332	0.91[EUR][1000 genomes]
rs11729602	0.89[EUR][1000 genomes]
rs11730169	0.89[EUR][1000 genomes]
rs11731942	0.95[EUR][1000 genomes]
rs11733311	0.86[EUR][1000 genomes]
rs11734524	0.89[EUR][1000 genomes]
rs11734860	0.96[EUR][1000 genomes]
rs11737447	0.88[EUR][1000 genomes]
rs13113113	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13117918	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13125295	0.97[EUR][1000 genomes]
rs13132939	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17382379	0.88[EUR][1000 genomes]
rs17382393	0.89[EUR][1000 genomes]
rs17466895	0.88[EUR][1000 genomes]
rs34250310	0.97[EUR][1000 genomes]
rs34276892	0.81[EUR][1000 genomes]
rs34352176	0.90[EUR][1000 genomes]
rs34949259	0.97[EUR][1000 genomes]
rs35041036	0.97[EUR][1000 genomes]
rs35161247	0.96[EUR][1000 genomes]
rs35509185	0.96[EUR][1000 genomes]
rs35515779	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35592594	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35617438	0.96[EUR][1000 genomes]
rs35870249	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35889107	0.93[EUR][1000 genomes]
rs3934645	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41264705	0.93[EUR][1000 genomes]
rs4443284	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4594724	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55698135	0.92[EUR][1000 genomes]
rs55740648	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56352084	0.86[EUR][1000 genomes]
rs58457272	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61036795	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62289276	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62289280	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62291980	0.88[EUR][1000 genomes]
rs62291983	0.91[EUR][1000 genomes]
rs62291984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs885260	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs885261	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
6	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
9	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:7797000-7807000	Weak transcription	Liver	Liver
12	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:7800200-7807200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:7800600-7806200	Weak transcription	Fetal Thymus	thymus
15	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:7801400-7807200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:7801400-7807400	Weak transcription	Right Ventricle	heart
18	chr4:7801800-7807400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:7802000-7806200	Weak transcription	Fetal Brain Male	brain
20	chr4:7802000-7807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:7802000-7807200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:7802000-7807800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:7802200-7806200	Weak transcription	Brain Substantia Nigra	brain
24	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:7802400-7806000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:7802400-7806200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:7802400-7806600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:7802400-7806800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:7802400-7812400	Weak transcription	Spleen	Spleen
30	chr4:7802600-7806000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:7802600-7806000	Weak transcription	Adipose Nuclei	Adipose
32	chr4:7802600-7806200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:7802600-7806400	Weak transcription	Fetal Brain Female	brain
34	chr4:7802600-7806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:7802600-7807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:7802600-7807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:7802600-7808000	Weak transcription	Gastric	stomach
38	chr4:7802600-7809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:7802600-7810400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:7802800-7806000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:7802800-7806000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:7802800-7806200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:7802800-7806400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:7802800-7806400	Weak transcription	Pancreas	Pancrea
45	chr4:7802800-7806600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:7802800-7806800	Weak transcription	Brain Germinal Matrix	brain
47	chr4:7802800-7807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:7802800-7807200	Weak transcription	Brain Anterior Caudate	brain
49	chr4:7802800-7807400	Weak transcription	Left Ventricle	heart
50	chr4:7802800-7807600	Weak transcription	Duodenum Mucosa	Duodenum

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