Variant report

Variant	rs2594554
Chromosome Location	chr3:81799871-81799872
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	chr3:81797791..81799957-chr3:81809417..81811244,2	MCF-7	breast:
2	chr3:81797341..81800582-chr3:81808703..81810715,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2316138	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594557	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594561	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680252	1.00[AMR][1000 genomes]
rs2680253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680255	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680256	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2680279	1.00[AMR][1000 genomes]
rs2680281	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2691074	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2691075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2691076	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2691087	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	esv3450476	chr3:81798912-81800910	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:81782200-81800400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:81782400-81800200	Weak transcription	Left Ventricle	heart
5	chr3:81791200-81808800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:81791600-81803400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:81792000-81810200	Weak transcription	Spleen	Spleen
8	chr3:81792800-81802800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:81793000-81802800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:81793000-81809600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:81793200-81803800	Weak transcription	Aorta	Aorta
12	chr3:81793200-81809200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:81793400-81801600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:81793400-81803600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:81793800-81800200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:81793800-81802600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:81793800-81808600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:81793800-81809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:81793800-81810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:81794000-81802800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:81794000-81807000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:81794200-81800200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:81794200-81803600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:81794400-81800600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:81794400-81808600	Weak transcription	K562	blood
26	chr3:81794800-81800200	Weak transcription	Liver	Liver
27	chr3:81794800-81807200	Weak transcription	HMEC	breast
28	chr3:81795600-81800000	Weak transcription	Psoas Muscle	Psoas
29	chr3:81795600-81800200	Weak transcription	Right Ventricle	heart
30	chr3:81795600-81800400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:81795600-81810000	Weak transcription	Lung	lung
32	chr3:81796000-81808600	Weak transcription	Small Intestine	intestine
33	chr3:81796200-81809200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:81796800-81800200	Weak transcription	HSMM	muscle
35	chr3:81796800-81802600	Weak transcription	Pancreas	Pancrea
36	chr3:81796800-81809200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:81797200-81804000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:81797400-81809800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:81797800-81800400	Strong transcription	Dnd41	blood
40	chr3:81797800-81803200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:81797800-81807200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:81798400-81800400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:81798400-81800400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:81798400-81809000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:81798600-81800200	Weak transcription	NHLF	lung
46	chr3:81798600-81801000	Strong transcription	HepG2	liver
47	chr3:81799000-81800200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:81799000-81800600	Weak transcription	Brain Substantia Nigra	brain
49	chr3:81799000-81808600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:81799200-81800400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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