Variant report

Variant	rs12712641
Chromosome Location	chr2:39619630-39619631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10169391	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.90[AFR][1000 genomes]
rs10170604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.90[AFR][1000 genomes]
rs10173722	0.80[AFR][1000 genomes]
rs10175333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.90[AFR][1000 genomes]
rs10865150	0.81[AFR][1000 genomes]
rs10865152	0.90[AFR][1000 genomes]
rs11124676	0.85[AFR][1000 genomes]
rs11124677	0.85[AFR][1000 genomes]
rs11124679	0.94[AFR][1000 genomes]
rs11124681	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.83[AFR][1000 genomes]
rs13028561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1468902	0.82[AFR][1000 genomes]
rs1474424	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.90[AFR][1000 genomes]
rs2005892	0.89[AFR][1000 genomes]
rs2056654	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160661	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2178762	0.93[AFR][1000 genomes]
rs2193422	0.90[AFR][1000 genomes]
rs2373534	0.80[AFR][1000 genomes]
rs2373536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.93[AFR][1000 genomes]
rs3770678	0.81[AFR][1000 genomes]
rs4670934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.92[AFR][1000 genomes]
rs6544223	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6718134	0.85[AFR][1000 genomes]
rs6724393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.89[AFR][1000 genomes]
rs6741312	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742170	0.90[AFR][1000 genomes]
rs6759495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.90[AFR][1000 genomes]
rs7578136	0.89[AFR][1000 genomes]
rs7579414	0.85[AFR][1000 genomes]
rs7582160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7601700	0.81[AFR][1000 genomes]
rs7603392	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7604047	0.83[AFR][1000 genomes]
rs7608153	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
4	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
8	chr2:39607600-39619800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
11	chr2:39608400-39621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
13	chr2:39609200-39621600	Weak transcription	Lung	lung
14	chr2:39609400-39621200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:39609400-39621200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:39609400-39621600	Weak transcription	HSMM	muscle
17	chr2:39609600-39621200	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:39609600-39621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:39609600-39621600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:39609600-39621600	Weak transcription	NH-A	brain
21	chr2:39609600-39621600	Weak transcription	Osteobl	bone
22	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:39610000-39621200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:39610200-39621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:39613000-39621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:39613400-39621200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:39613600-39621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:39613600-39621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:39614000-39619800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:39614800-39620800	Weak transcription	Right Ventricle	heart
34	chr2:39614800-39621600	Weak transcription	Pancreas	Pancrea
35	chr2:39615600-39621400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:39615800-39621200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:39616000-39620200	Weak transcription	Fetal Lung	lung
39	chr2:39616000-39620800	Weak transcription	Left Ventricle	heart
40	chr2:39616000-39621200	Weak transcription	Aorta	Aorta
41	chr2:39616000-39622200	Weak transcription	Fetal Stomach	stomach
42	chr2:39616000-39626400	Weak transcription	Gastric	stomach
43	chr2:39616800-39619800	Weak transcription	HepG2	liver
44	chr2:39616800-39621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:39617400-39620400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:39617600-39621200	Weak transcription	Fetal Heart	heart
47	chr2:39617600-39626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:39617800-39620800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:39617800-39621200	Weak transcription	Rectal Smooth Muscle	rectum

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