Variant report

Variant	rs10497620
Chromosome Location	chr2:183992507-183992508
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183775532..183777640-chr2:183990491..183993127,2	K562	blood:
2	chr2:183992197..183994349-chr2:184006346..184008645,2	K562	blood:
3	chr2:183989126..183990874-chr2:183990952..183992681,2	MCF-7	breast:
4	chr2:183990685..183993122-chr2:184003291..184005876,2	K562	blood:
5	chr2:183942911..183945636-chr2:183991182..183993608,2	K562	blood:

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction
ENSG00000162999	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11682917	0.91[ASN][1000 genomes]
rs11893835	0.81[ASN][1000 genomes]
rs11904393	0.81[ASN][1000 genomes]
rs1400132	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1462534	0.89[ASN][1000 genomes]
rs16823723	0.96[ASN][1000 genomes]
rs16824018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824048	0.96[ASN][1000 genomes]
rs16824058	0.96[ASN][1000 genomes]
rs16824059	0.96[ASN][1000 genomes]
rs16824095	0.96[ASN][1000 genomes]
rs16824106	0.96[ASN][1000 genomes]
rs17706149	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17757841	0.81[ASN][1000 genomes]
rs1997486	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017742	1.00[ASN][1000 genomes]
rs2176232	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2254879	0.82[YRI][hapmap]
rs2368373	1.00[ASN][1000 genomes]
rs2675094	0.86[ASN][1000 genomes]
rs2887234	0.86[CHB][hapmap]
rs35453132	0.80[ASN][1000 genomes]
rs3748881	0.96[ASN][1000 genomes]
rs3748882	0.96[ASN][1000 genomes]
rs3762476	0.96[ASN][1000 genomes]
rs4372840	0.80[ASN][1000 genomes]
rs4467235	0.81[ASN][1000 genomes]
rs4606882	0.96[ASN][1000 genomes]
rs4666611	0.96[ASN][1000 genomes]
rs4666612	0.96[ASN][1000 genomes]
rs4666620	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666890	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666892	0.96[ASN][1000 genomes]
rs4666896	0.93[ASN][1000 genomes]
rs4666898	0.93[ASN][1000 genomes]
rs55657876	0.83[AFR][1000 genomes]
rs55696219	0.83[AFR][1000 genomes]
rs55957340	0.83[AFR][1000 genomes]
rs56402172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712479	0.83[AFR][1000 genomes]
rs6736682	0.81[ASN][1000 genomes]
rs72892678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892681	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892682	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892683	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892686	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72892687	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72892688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892689	0.83[AFR][1000 genomes]
rs72892690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892694	0.83[AFR][1000 genomes]
rs72892702	0.83[AFR][1000 genomes]
rs72894503	0.83[AFR][1000 genomes]
rs72894513	0.83[AFR][1000 genomes]
rs72894514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894527	0.83[AFR][1000 genomes]
rs72894533	0.83[AFR][1000 genomes]
rs72894535	0.83[AFR][1000 genomes]
rs72894537	0.83[AFR][1000 genomes]
rs72894544	0.83[AFR][1000 genomes]
rs72894546	0.83[AFR][1000 genomes]
rs72894558	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72894593	0.83[AFR][1000 genomes]
rs72896534	0.83[AFR][1000 genomes]
rs72896567	0.83[AFR][1000 genomes]
rs72896586	0.83[AFR][1000 genomes]
rs72896596	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72896599	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72898512	0.83[AFR][1000 genomes]
rs72898513	0.83[AFR][1000 genomes]
rs72898514	0.83[AFR][1000 genomes]
rs72898532	0.83[AFR][1000 genomes]
rs72898539	0.83[AFR][1000 genomes]
rs7562034	0.83[AFR][1000 genomes]
rs7567370	0.83[AFR][1000 genomes]
rs7577407	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7591252	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9333281	1.00[ASN][1000 genomes]
rs9333283	1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking 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	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv2763287	chr2:183939173-184037893	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183990000-183996200	Weak transcription	Lung	lung
2	chr2:183990000-184003600	Weak transcription	Left Ventricle	heart
3	chr2:183990000-184008600	Weak transcription	Esophagus	oesophagus
4	chr2:183990000-184008800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:183990000-184024400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:183990000-184050000	Weak transcription	Aorta	Aorta
7	chr2:183990200-183993600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:183990200-183995000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:183990200-184008200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:183990200-184014200	Weak transcription	HSMMtube	muscle
11	chr2:183990200-184018800	Weak transcription	Placenta	Placenta
12	chr2:183990200-184036400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:183990600-183992600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr2:183990600-183994400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:183990600-183995400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:183990600-183995600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:183990600-183995800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:183990600-184010200	Weak transcription	Brain Substantia Nigra	brain
19	chr2:183990600-184028600	Weak transcription	Colonic Mucosa	Colon
20	chr2:183990800-183993000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:183990800-183994400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:183990800-183994400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:183990800-183995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:183990800-184000000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:183990800-184025800	Weak transcription	Fetal Kidney	kidney
26	chr2:183990800-184031000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:183991000-183992600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:183991000-183993000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:183991000-183993000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:183991000-183993000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:183991000-183993000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:183991000-183993000	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:183991000-183993000	Weak transcription	HSMM	muscle
34	chr2:183991000-183993200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:183991000-183993200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:183991000-183993200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:183991000-183993400	Weak transcription	Psoas Muscle	Psoas
38	chr2:183991000-183993600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:183991000-183993600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:183991000-183993800	Weak transcription	NH-A	brain
41	chr2:183991000-183994200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:183991000-183994400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:183991000-183995000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:183991000-183995200	Weak transcription	Thymus	Thymus
45	chr2:183991000-183995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:183991000-183995600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:183991000-183996000	Weak transcription	Fetal Heart	heart
48	chr2:183991000-184008000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:183991000-184008400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:183991000-184013400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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