Variant report

Variant	rs2138259
Chromosome Location	chr3:120061234-120061235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120060316..120061973-chr3:120090853..120092791,2	MCF-7	breast:
2	chr3:120059782..120066077-chr3:120066537..120070898,10	K562	blood:
3	chr3:120047929..120050381-chr3:120059244..120062451,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1085612	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1085613	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1092829	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147682	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1147683	0.90[AFR][1000 genomes]
rs1147686	0.90[AFR][1000 genomes]
rs1147687	0.90[AFR][1000 genomes]
rs1147691	0.90[AFR][1000 genomes]
rs1147692	0.90[AFR][1000 genomes]
rs1147704	0.85[AFR][1000 genomes]
rs11717787	0.83[ASN][1000 genomes]
rs1259290	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1259297	0.81[AFR][1000 genomes]
rs12638445	0.91[ASN][1000 genomes]
rs1515576	0.99[ASN][1000 genomes]
rs1588890	0.90[AFR][1000 genomes]
rs1588891	0.90[AFR][1000 genomes]
rs1606872	0.85[AFR][1000 genomes]
rs1606873	0.90[AFR][1000 genomes]
rs1615793	0.90[AFR][1000 genomes]
rs1623323	0.90[AFR][1000 genomes]
rs1716846	0.90[AFR][1000 genomes]
rs1733325	0.90[AFR][1000 genomes]
rs1733327	0.90[AFR][1000 genomes]
rs1733329	0.90[AFR][1000 genomes]
rs1733331	0.90[AFR][1000 genomes]
rs1733353	0.90[AFR][1000 genomes]
rs1733354	0.90[AFR][1000 genomes]
rs1849933	0.80[EUR][1000 genomes]
rs2030413	0.86[ASN][1000 genomes]
rs2638592	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2673704	0.81[AFR][1000 genomes]
rs2700260	0.81[AFR][1000 genomes]
rs2702156	0.90[AFR][1000 genomes]
rs2702164	0.90[AFR][1000 genomes]
rs2943754	0.90[AFR][1000 genomes]
rs6438576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622363	0.97[ASN][1000 genomes]
rs787197	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs787199	0.85[ASN][1000 genomes]
rs787201	0.85[ASN][1000 genomes]
rs787210	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805080	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs810888	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs939499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950649	0.90[AFR][1000 genomes]
rs950650	0.90[AFR][1000 genomes]
rs9851825	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription 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 miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2138259	LOC100130701	cis	brain	BrainEAC

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
2	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:120044400-120066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:120045200-120066800	Weak transcription	Stomach Mucosa	stomach
5	chr3:120045600-120066800	Weak transcription	Colonic Mucosa	Colon
6	chr3:120048400-120066800	Weak transcription	Right Ventricle	heart
7	chr3:120048600-120063000	Weak transcription	HSMMtube	muscle
8	chr3:120050400-120066000	Weak transcription	Fetal Brain Male	brain
9	chr3:120051000-120063800	Weak transcription	NHLF	lung
10	chr3:120051000-120067000	Weak transcription	Esophagus	oesophagus
11	chr3:120051200-120065600	Weak transcription	HMEC	breast
12	chr3:120051200-120066800	Weak transcription	Psoas Muscle	Psoas
13	chr3:120051200-120066800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:120051800-120065600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:120052600-120067000	Weak transcription	Left Ventricle	heart
16	chr3:120052800-120064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:120053000-120062400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:120053000-120062800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:120053200-120061600	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:120053200-120063000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:120053200-120065200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:120053200-120066600	Weak transcription	Fetal Kidney	kidney
23	chr3:120053800-120066600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:120053800-120066600	Weak transcription	NH-A	brain
25	chr3:120054000-120063400	Weak transcription	Osteobl	bone
26	chr3:120054000-120066000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:120054200-120061600	Weak transcription	HSMM	muscle
28	chr3:120054200-120063000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:120054200-120063200	Weak transcription	NHDF-Ad	bronchial
30	chr3:120054200-120064600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:120054200-120065600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:120054200-120065600	Weak transcription	Fetal Heart	heart
33	chr3:120054200-120065600	Weak transcription	NHEK	skin
34	chr3:120054200-120066600	Weak transcription	HUVEC	blood vessel
35	chr3:120054200-120066600	Weak transcription	K562	blood
36	chr3:120054400-120063000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:120054800-120062600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:120055000-120061800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:120055200-120064200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:120055600-120062800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:120056200-120062000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:120056400-120062000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:120056800-120062000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr3:120057400-120062200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr3:120057400-120062600	ZNF genes & repeats	GM12878-XiMat	blood
46	chr3:120057800-120063000	Weak transcription	Primary T cells from cord blood	blood
47	chr3:120057800-120067000	Weak transcription	Small Intestine	intestine
48	chr3:120058000-120062400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:120058200-120062600	ZNF genes & repeats	Dnd41	blood
50	chr3:120058400-120061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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