Variant report

Variant	rs9882962
Chromosome Location	chr3:48573311-48573312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48488203..48490613-chr3:48571526..48574368,2	K562	blood:
2	chr3:48571448..48573714-chr3:48576001..48578662,2	MCF-7	breast:
3	chr3:48572206..48574308-chr3:48584630..48587149,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164053	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003649	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs10049154	0.83[EUR][1000 genomes]
rs10470687	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13060933	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs13063312	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs13064619	0.83[EUR][1000 genomes]
rs13069724	0.83[YRI][hapmap]
rs13070798	0.83[GIH][hapmap]
rs13091944	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13100178	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13319635	0.85[ASN][1000 genomes]
rs13319651	0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs13324142	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs2006871	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276850	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap]
rs2310996	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs2854394	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs2854395	0.82[ASN][1000 genomes]
rs28563843	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28581474	0.81[ASN][1000 genomes]
rs28881595	0.83[EUR][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35562294	0.83[ASN][1000 genomes]
rs3755819	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821876	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs3969942	0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4075082	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442127	0.83[EUR][1000 genomes]
rs6781283	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6785845	0.83[EUR][1000 genomes]
rs6786424	0.83[EUR][1000 genomes]
rs6792156	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs6792525	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806059	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6809981	0.83[EUR][1000 genomes]
rs740787	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs7428949	0.81[ASN][1000 genomes]
rs7434077	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs7434107	0.81[ASN][1000 genomes]
rs7623614	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7631574	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs7640031	0.81[ASN][1000 genomes]
rs7644771	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9810991	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9822677	0.83[EUR][1000 genomes]
rs9830581	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs9835827	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs9836462	0.83[GIH][hapmap]
rs9837687	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs9848824	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9849280	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9851743	0.81[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862906	1.00[AMR][1000 genomes]
rs9864729	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869698	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9871608	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875911	0.88[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9878950	0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs9881877	0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:48555400-48578000	Strong transcription	HepG2	liver
4	chr3:48556200-48580400	Weak transcription	HSMMtube	muscle
5	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:48559400-48575200	Weak transcription	Small Intestine	intestine
8	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
9	chr3:48560600-48578200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:48560800-48577800	Strong transcription	GM12878-XiMat	blood
11	chr3:48561000-48578200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:48561200-48574400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:48565800-48583600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:48567000-48575400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:48568000-48577200	Strong transcription	Placenta	Placenta
17	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:48569000-48579200	Weak transcription	Thymus	Thymus
19	chr3:48569200-48578000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:48569800-48577600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:48569800-48578200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:48570000-48578000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:48570000-48578000	Strong transcription	Brain Germinal Matrix	brain
24	chr3:48570000-48578000	Strong transcription	Fetal Brain Female	brain
25	chr3:48570000-48578000	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr3:48570400-48577800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:48570400-48580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
29	chr3:48571000-48578200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:48571000-48581800	Strong transcription	Fetal Intestine Small	intestine
31	chr3:48571200-48576000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:48571200-48578000	Strong transcription	Fetal Stomach	stomach
33	chr3:48571400-48576800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:48571400-48577600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:48571400-48577600	Strong transcription	Brain Hippocampus Middle	brain
36	chr3:48571400-48577600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:48571400-48578000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:48571400-48580600	Weak transcription	Left Ventricle	heart
39	chr3:48571600-48574400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:48571600-48576200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:48571800-48573800	Weak transcription	A549	lung
42	chr3:48571800-48577200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr3:48571800-48577600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:48571800-48578000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:48571800-48579400	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:48572000-48574400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr3:48572000-48575000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:48572000-48577200	Strong transcription	Ovary	ovary
49	chr3:48572000-48579600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:48572200-48583800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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