Variant report

Variant	rs2609871
Chromosome Location	chr3:146247286-146247287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:146246213-146247344	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146246635..146248692-chr3:146260793..146263369,2	MCF-7	breast:
2	chr3:146245382..146249214-chr3:146253354..146257434,4	K562	blood:

Variant related genes	Relation type
PLSCR1	TF binding region
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2587025	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2587026	0.81[ASN][1000 genomes]
rs2587027	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2587029	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2609872	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2688692	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688693	0.94[JPT][hapmap]
rs2738908	0.95[JPT][hapmap]
rs2738909	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146224800-146254400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:146225400-146255000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:146225400-146256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:146225400-146257000	Weak transcription	Right Ventricle	heart
5	chr3:146225400-146260800	Weak transcription	NH-A	brain
6	chr3:146225600-146252200	Weak transcription	Psoas Muscle	Psoas
7	chr3:146225600-146258600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:146228000-146248200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:146229000-146253200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:146229400-146252200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:146229800-146257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:146230400-146248600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:146231600-146250800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:146231600-146254400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:146231600-146254400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:146231600-146257200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:146231600-146258600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:146231600-146259000	Weak transcription	Brain Angular Gyrus	brain
20	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:146231800-146254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:146231800-146254400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:146232000-146257400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
25	chr3:146232600-146248400	Weak transcription	HMEC	breast
26	chr3:146232800-146248600	Weak transcription	Aorta	Aorta
27	chr3:146232800-146250200	Weak transcription	Pancreas	Pancrea
28	chr3:146232800-146254400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:146232800-146256000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:146233000-146248400	Weak transcription	Colonic Mucosa	Colon
31	chr3:146233000-146248600	Weak transcription	NHEK	skin
32	chr3:146233000-146248800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:146233000-146255200	Weak transcription	Esophagus	oesophagus
34	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:146233600-146259200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:146234400-146258000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:146235800-146248600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:146235800-146251600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:146236200-146254400	Weak transcription	Gastric	stomach
41	chr3:146236200-146254600	Weak transcription	Spleen	Spleen
42	chr3:146236800-146250000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:146237000-146253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:146237000-146254400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:146237200-146252200	Strong transcription	Dnd41	blood
46	chr3:146237200-146253000	Strong transcription	Fetal Thymus	thymus
47	chr3:146237200-146253400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:146237400-146254400	Weak transcription	Stomach Mucosa	stomach
49	chr3:146239800-146251400	Weak transcription	HSMMtube	muscle
50	chr3:146240000-146248200	Weak transcription	HSMM	muscle

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