Variant report

Variant	rs11124681
Chromosome Location	chr2:39649654-39649655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39647976..39656890-chr2:39661783..39666548,15	MCF-7	breast:
2	chr2:39646458..39648689-chr2:39648799..39652101,4	K562	blood:
3	chr2:39643207..39646078-chr2:39648407..39650074,2	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10169391	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10170424	0.91[AFR][1000 genomes]
rs10170604	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10173556	0.83[AFR][1000 genomes]
rs10175333	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10181650	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10196253	0.94[ASN][1000 genomes]
rs1035232	0.82[AFR][1000 genomes]
rs10865152	0.82[AFR][1000 genomes]
rs11124679	0.86[AFR][1000 genomes]
rs11688998	0.94[ASN][1000 genomes]
rs12614034	0.83[AFR][1000 genomes]
rs12712641	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13028561	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1474424	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1477164	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17023504	0.89[ASN][1000 genomes]
rs17023656	0.94[ASN][1000 genomes]
rs17023777	0.94[ASN][1000 genomes]
rs1922827	0.82[AFR][1000 genomes]
rs2005892	0.81[AFR][1000 genomes]
rs2056654	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2111382	0.83[AMR][1000 genomes]
rs2160661	0.83[AMR][1000 genomes]
rs2178762	0.85[AFR][1000 genomes]
rs2193422	0.82[AFR][1000 genomes]
rs2373536	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2888598	0.85[AFR][1000 genomes]
rs3755175	0.89[ASN][1000 genomes]
rs3770676	0.89[ASN][1000 genomes]
rs3770677	0.89[ASN][1000 genomes]
rs3770679	0.89[ASN][1000 genomes]
rs4670934	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4670935	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4670936	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55748017	0.89[ASN][1000 genomes]
rs56833014	0.94[ASN][1000 genomes]
rs57103739	0.89[ASN][1000 genomes]
rs57232122	0.94[ASN][1000 genomes]
rs58704884	0.94[ASN][1000 genomes]
rs60192971	0.94[ASN][1000 genomes]
rs61480659	0.94[ASN][1000 genomes]
rs6419603	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6544222	0.84[AFR][1000 genomes]
rs6544223	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6544226	1.00[ASN][1000 genomes]
rs6544228	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6717792	0.89[AFR][1000 genomes]
rs6724393	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6730902	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6732611	0.92[AFR][1000 genomes]
rs6741312	0.83[AMR][1000 genomes]
rs6742170	0.82[AFR][1000 genomes]
rs6759495	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6760382	0.82[AFR][1000 genomes]
rs7578136	0.81[AFR][1000 genomes]
rs7582160	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7591102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7595041	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7603392	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7604047	0.80[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	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
2	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
3	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
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39636600-39651400	Weak transcription	Fetal Thymus	thymus
2	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:39637600-39651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:39638800-39652400	Weak transcription	Hela-S3	cervix
5	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
6	chr2:39639600-39657200	Weak transcription	HMEC	breast
7	chr2:39640800-39652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39640800-39656800	Weak transcription	NH-A	brain
9	chr2:39640800-39660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:39641000-39651600	Weak transcription	HSMMtube	muscle
11	chr2:39641000-39656600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:39641200-39650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:39641200-39659600	Weak transcription	Brain Angular Gyrus	brain
14	chr2:39644200-39650000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:39644400-39654200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:39644400-39654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:39644800-39650600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:39645000-39651400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:39645000-39658800	Weak transcription	Brain Anterior Caudate	brain
21	chr2:39645200-39651600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:39645200-39658200	Weak transcription	Right Ventricle	heart
23	chr2:39645400-39651400	Weak transcription	Left Ventricle	heart
24	chr2:39646000-39652400	Weak transcription	Brain Substantia Nigra	brain
25	chr2:39646000-39660200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:39646200-39650400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:39646200-39651600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:39646200-39652000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:39646200-39653200	Weak transcription	Stomach Mucosa	stomach
30	chr2:39646200-39656200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:39646200-39658000	Weak transcription	Liver	Liver
32	chr2:39647000-39657400	Weak transcription	Adipose Nuclei	Adipose
33	chr2:39647200-39651600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:39647200-39652600	Weak transcription	Fetal Heart	heart
35	chr2:39647200-39658400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:39647200-39659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:39647400-39650200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:39647400-39650200	Weak transcription	NHLF	lung
39	chr2:39647400-39650400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:39647400-39651600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:39647400-39651600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:39647400-39651600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:39647400-39651600	Weak transcription	A549	lung
44	chr2:39647400-39651600	Weak transcription	HSMM	muscle
45	chr2:39647400-39652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:39647400-39652000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:39647400-39652400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:39647400-39654200	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:39647400-39656600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:39647400-39657800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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