Variant report

Variant	rs2289348
Chromosome Location	chr3:139164266-139164267
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	chr3:139156554..139158574-chr3:139162722..139165410,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS22-1	chr3:139163021-139165157	NONHSAT092369

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1602626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1602628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17316181	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17335312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17394620	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17395611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17494356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17494482	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17560106	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184156	1.00[JPT][hapmap]
rs184157	0.82[JPT][hapmap]
rs2233818	0.81[AFR][1000 genomes]
rs2289350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2307031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2882080	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2882081	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs295490	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs3772871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs397940	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs41356949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41399544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55922868	0.85[ASN][1000 genomes]
rs56993164	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57707457	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57995350	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58060926	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59628512	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59958973	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59960641	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61034702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61613889	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61680644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6795778	0.82[YRI][hapmap]
rs7428398	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9821204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9837167	0.81[ASN][1000 genomes]
rs9862672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2760754	chr3:139144615-139164874	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
2	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
6	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
7	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
8	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:139145200-139164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:139149800-139170600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:139154000-139167000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:139154200-139165600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:139154200-139168200	Weak transcription	Fetal Intestine Small	intestine
15	chr3:139154200-139171200	Weak transcription	Right Atrium	heart
16	chr3:139154200-139173600	Weak transcription	Ovary	ovary
17	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
18	chr3:139154400-139166200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:139154400-139167000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:139154800-139165200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:139158600-139166200	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:139158600-139172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:139158600-139174800	Weak transcription	Adipose Nuclei	Adipose
24	chr3:139158800-139166000	Weak transcription	HSMMtube	muscle
25	chr3:139160200-139174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:139160600-139170200	Weak transcription	Lung	lung
27	chr3:139160600-139174800	Weak transcription	Fetal Brain Male	brain
28	chr3:139161000-139164800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:139161400-139166200	Weak transcription	Brain Germinal Matrix	brain
30	chr3:139161400-139168800	Weak transcription	Fetal Intestine Large	intestine
31	chr3:139162800-139164400	Enhancers	Brain Angular Gyrus	brain
32	chr3:139162800-139166600	Enhancers	Brain Hippocampus Middle	brain
33	chr3:139162800-139167600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:139163000-139170000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
36	chr3:139163800-139165400	Weak transcription	Brain Anterior Caudate	brain
37	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:139164200-139165000	Weak transcription	Brain Substantia Nigra	brain

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