Variant report

Variant	rs3794878
Chromosome Location	chr18:29219289-29219290
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	chr18:29219249..29221553-chr18:29225572..29227383,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1026122	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1026123	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1078998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12962843	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1612691	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1621308	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1667262	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1667274	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667275	0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1667276	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667279	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667280	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667281	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667283	0.91[ASN][1000 genomes]
rs1667284	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1667286	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1667287	0.81[ASN][1000 genomes]
rs1791161	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1791169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1791171	0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1791181	0.88[ASN][1000 genomes]
rs1791192	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1791193	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1791221	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2595360	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794882	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41447647	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4799311	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6506935	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232056	0.86[EUR][1000 genomes]
rs7242641	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8097755	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895888	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs974676	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs974677	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9950458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29194800-29226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:29197600-29224800	Weak transcription	Brain Anterior Caudate	brain
3	chr18:29197600-29224800	Weak transcription	Brain Germinal Matrix	brain
4	chr18:29200000-29222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr18:29200200-29222000	Weak transcription	HMEC	breast
6	chr18:29202800-29235000	Weak transcription	Pancreas	Pancrea
7	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:29203800-29220200	Weak transcription	Ovary	ovary
9	chr18:29203800-29226000	Weak transcription	Fetal Lung	lung
10	chr18:29203800-29227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:29204000-29228400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:29204200-29223200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr18:29204400-29220800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:29204400-29228400	Weak transcription	Psoas Muscle	Psoas
15	chr18:29204600-29238600	Weak transcription	Gastric	stomach
16	chr18:29205000-29227400	Weak transcription	A549	lung
17	chr18:29206800-29225800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr18:29208000-29227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr18:29208200-29223200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:29208400-29227000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:29208400-29229000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr18:29208800-29222600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr18:29209000-29226000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr18:29209000-29228400	Weak transcription	Brain Angular Gyrus	brain
25	chr18:29210000-29223400	Weak transcription	Adipose Nuclei	Adipose
26	chr18:29210800-29224600	Weak transcription	Fetal Intestine Small	intestine
27	chr18:29211000-29223200	Weak transcription	Fetal Brain Female	brain
28	chr18:29211000-29227400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr18:29211200-29221600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:29211200-29224800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr18:29211200-29225800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:29211200-29226000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr18:29211200-29227400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:29213800-29229000	Weak transcription	HUVEC	blood vessel
35	chr18:29214400-29226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:29214600-29225800	Weak transcription	Fetal Thymus	thymus
37	chr18:29214800-29228800	Weak transcription	NH-A	brain
38	chr18:29216000-29219400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr18:29216000-29219400	ZNF genes & repeats	GM12878-XiMat	blood
40	chr18:29216000-29221200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:29216000-29224600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr18:29216000-29229000	Weak transcription	Placenta	Placenta
43	chr18:29216400-29220200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr18:29217200-29221000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr18:29218800-29222600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:29218800-29232200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr18:29219200-29220600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr18:29219200-29220600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:29219200-29222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr18:29219200-29223800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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