Variant report

Variant	rs10002261
Chromosome Location	chr4:53488862-53488863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53486430..53489382-chr4:53494314..53496230,2	K562	blood:
2	chr4:53486430..53489345-chr4:53494314..53496043,3	K562	blood:
3	chr4:53487992..53490460-chr4:53523831..53526768,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109189	Chromatin interaction
ENSG00000248866	Chromatin interaction

Extended variants
information (count: 65 )
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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10010306	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10027906	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]
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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][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];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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:8 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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:106 , 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	chr4:53456000-53506400	Weak transcription	HUVEC	blood vessel
3	chr4:53463000-53507200	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:53463800-53494000	Weak transcription	NHLF	lung
5	chr4:53464200-53494800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:53464200-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:53468200-53510200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:53468600-53493600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:53468600-53497600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:53472600-53499000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:53473000-53506800	Weak transcription	Primary T cells from cord blood	blood
12	chr4:53473600-53491400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:53473600-53507200	Weak transcription	Osteobl	bone
14	chr4:53473800-53490600	Weak transcription	HSMMtube	muscle
15	chr4:53475000-53501200	Weak transcription	Gastric	stomach
16	chr4:53476000-53489000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:53476000-53491400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:53476000-53494200	Weak transcription	Lung	lung
19	chr4:53476000-53496200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:53476000-53502200	Weak transcription	Pancreas	Pancrea
21	chr4:53476000-53507400	Weak transcription	HSMM	muscle
22	chr4:53476200-53489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:53476600-53491000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:53476600-53501600	Weak transcription	HepG2	liver
25	chr4:53476800-53490800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:53476800-53491200	Weak transcription	Placenta	Placenta
27	chr4:53476800-53491400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:53476800-53494200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:53476800-53494200	Weak transcription	HMEC	breast
30	chr4:53477000-53491600	Weak transcription	Liver	Liver
31	chr4:53477200-53491000	Weak transcription	Adipose Nuclei	Adipose
32	chr4:53477400-53489800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:53477400-53491600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:53477600-53510200	Weak transcription	Esophagus	oesophagus
35	chr4:53479400-53490400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:53479400-53491600	Weak transcription	Ovary	ovary
37	chr4:53479400-53494200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:53479600-53491200	Weak transcription	Left Ventricle	heart
39	chr4:53479800-53490800	Weak transcription	Right Ventricle	heart
40	chr4:53479800-53499800	Weak transcription	Right Atrium	heart
41	chr4:53480800-53499800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:53480800-53501200	Weak transcription	GM12878-XiMat	blood
43	chr4:53482200-53492000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:53484400-53490800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:53484600-53508400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:53485200-53498000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:53485400-53495800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:53485400-53497600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr4:53485400-53499400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:53485600-53491600	Weak transcription	Brain Anterior Caudate	brain

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