Variant report

Variant	rs2291378
Chromosome Location	chr3:105219511-105219512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105215069..105217768-chr3:105217819..105220349,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16851098	0.89[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs16851279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs2062433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291377	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772555	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs3821492	0.85[MEX][hapmap]
rs3910551	0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs41380949	0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs56341088	0.86[ASN][1000 genomes]
rs62260777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262966	0.89[AMR][1000 genomes]
rs62262967	0.87[AMR][1000 genomes]
rs62262968	0.87[AMR][1000 genomes]
rs7624892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS 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 target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210000-105223000	Weak transcription	Gastric	stomach
2	chr3:105210200-105220600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:105210200-105220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:105210200-105221200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:105210200-105222000	Weak transcription	NH-A	brain
6	chr3:105210200-105223800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:105210200-105229000	Weak transcription	HSMM	muscle
8	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:105210400-105219600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:105210600-105219600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:105210600-105223200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:105210800-105222400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:105213800-105219600	Weak transcription	Aorta	Aorta
14	chr3:105214200-105220000	Weak transcription	Osteobl	bone
15	chr3:105214400-105219600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:105214400-105220600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:105215600-105219600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:105215600-105219800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:105215600-105221200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:105215600-105223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:105215800-105223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:105215800-105223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:105217400-105220200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:105218200-105220600	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:105218200-105221200	Enhancers	HepG2	liver
26	chr3:105218200-105221400	Enhancers	Liver	Liver
27	chr3:105218200-105222000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:105218400-105219800	Enhancers	A549	lung
29	chr3:105218400-105220200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:105218400-105220200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:105218400-105220200	Enhancers	Fetal Heart	heart
32	chr3:105218600-105219800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:105218600-105220200	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:105218600-105222400	Enhancers	Brain Angular Gyrus	brain
35	chr3:105218800-105219800	Weak transcription	Fetal Lung	lung
36	chr3:105218800-105221200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:105219000-105221400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:105219000-105222000	Weak transcription	Fetal Kidney	kidney
39	chr3:105219200-105219600	Weak transcription	Stomach Mucosa	stomach
40	chr3:105219200-105220200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:105219400-105219800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:105219400-105220200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:105219400-105220200	Enhancers	Brain Anterior Caudate	brain

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