Variant report

Variant	rs10027906
Chromosome Location	chr4:53474416-53474417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53473032..53474640-chr4:53524220..53526096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248866	Chromatin interaction
ENSG00000109189	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10001370	0.90[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10010306	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10012676	1.00[AMR][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	0.90[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10021143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10023867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10028085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10028755	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10029145	0.97[ASN][1000 genomes]
rs10031386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10033218	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10471216	0.90[ASN][1000 genomes]
rs13434726	1.00[AMR][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28376189	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28379922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28380682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28396506	1.00[AMR][1000 genomes]
rs28402205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28411005	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28412170	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28430452	0.90[ASN][1000 genomes]
rs28451750	0.97[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28478374	1.00[AMR][1000 genomes]
rs28482298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28503210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28565016	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28588481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28590396	0.90[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28644292	0.97[ASN][1000 genomes]
rs28654693	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660571	0.90[ASN][1000 genomes]
rs28672279	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28694544	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28721897	0.90[ASN][1000 genomes]
rs28722174	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28784684	0.90[ASN][1000 genomes]
rs28825181	1.00[ASN][1000 genomes]
rs28825412	0.90[ASN][1000 genomes]
rs28849759	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28852068	0.90[ASN][1000 genomes]
rs6830833	0.90[ASN][1000 genomes]
rs7673679	0.86[ASN][1000 genomes]
rs9990686	0.90[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9997863	0.90[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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv482581	chr4:53310749-53480710	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53451800-53501400	Weak transcription	Small Intestine	intestine
2	chr4:53453000-53485400	Weak transcription	Psoas Muscle	Psoas
3	chr4:53454800-53485400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:53456000-53506400	Weak transcription	HUVEC	blood vessel
5	chr4:53456600-53482000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:53458200-53478800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:53458800-53485000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:53459000-53483600	Weak transcription	K562	blood
9	chr4:53459200-53477400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr4:53459600-53477400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:53460800-53476800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:53461000-53477000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:53461200-53477600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:53461200-53478800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:53461400-53481800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:53461400-53488200	Weak transcription	NHDF-Ad	bronchial
17	chr4:53461600-53477600	Weak transcription	Colonic Mucosa	Colon
18	chr4:53461600-53481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:53462000-53477400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:53462600-53476800	Strong transcription	Placenta	Placenta
21	chr4:53463000-53507200	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:53463200-53474600	Weak transcription	GM12878-XiMat	blood
23	chr4:53463600-53476400	Weak transcription	HMEC	breast
24	chr4:53463600-53483600	Weak transcription	Fetal Brain Male	brain
25	chr4:53463800-53474600	Weak transcription	Pancreas	Pancrea
26	chr4:53463800-53480800	Weak transcription	Dnd41	blood
27	chr4:53463800-53483800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:53463800-53494000	Weak transcription	NHLF	lung
29	chr4:53464200-53474800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:53464200-53488600	Weak transcription	NHEK	skin
31	chr4:53464200-53494800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:53464200-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:53465400-53479800	Strong transcription	Fetal Stomach	stomach
34	chr4:53466600-53476800	Strong transcription	Primary B cells from cord blood	blood
35	chr4:53466800-53480000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:53467000-53478000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:53467400-53477200	Weak transcription	Right Atrium	heart
38	chr4:53468200-53474600	Weak transcription	Gastric	stomach
39	chr4:53468200-53485000	Weak transcription	Stomach Mucosa	stomach
40	chr4:53468200-53510200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:53468400-53475600	Weak transcription	HSMM	muscle
42	chr4:53468400-53485200	Weak transcription	Brain Substantia Nigra	brain
43	chr4:53468600-53475000	Weak transcription	HepG2	liver
44	chr4:53468600-53493600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:53468600-53497600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:53468800-53474600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:53468800-53475600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:53468800-53477400	Weak transcription	Aorta	Aorta
49	chr4:53468800-53479200	Weak transcription	Spleen	Spleen
50	chr4:53469000-53474600	Weak transcription	Brain Germinal Matrix	brain

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