Variant report

Variant	rs332844
Chromosome Location	chr19:38642044-38642045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38634157..38637003-chr19:38638873..38642073,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10404957	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654366	0.83[JPT][hapmap]
rs1654369	0.83[ASN][1000 genomes]
rs1725472	0.83[JPT][hapmap]
rs1725489	0.94[JPT][hapmap]
rs2005055	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099340	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278429	0.85[CEU][hapmap]
rs2384778	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2569412	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332848	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332849	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332850	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332851	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332855	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332856	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332858	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332864	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35932728	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802251	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508765	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705507	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8100128	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8100144	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101826	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109799	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112798	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs855614	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855632	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9941474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
6	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
8	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
13	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
14	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
15	chr19:38621600-38642800	Weak transcription	NHLF	lung
16	chr19:38623000-38642800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
18	chr19:38626000-38643400	Weak transcription	Placenta	Placenta
19	chr19:38626400-38643400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:38626400-38652200	Strong transcription	A549	lung
21	chr19:38626600-38643600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:38626800-38646000	Weak transcription	HMEC	breast
23	chr19:38627000-38652400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:38627600-38642800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:38628400-38652600	Weak transcription	Right Atrium	heart
26	chr19:38628600-38645000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:38628800-38645200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr19:38628800-38646400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr19:38628800-38651200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:38629200-38652600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:38629600-38651600	Strong transcription	GM12878-XiMat	blood
32	chr19:38633000-38651000	Strong transcription	Primary B cells from cord blood	blood
33	chr19:38633000-38652400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:38633200-38652800	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:38633400-38650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:38633400-38653000	Weak transcription	Fetal Brain Male	brain
37	chr19:38634200-38642200	Weak transcription	Ovary	ovary
38	chr19:38634200-38643200	Weak transcription	Fetal Lung	lung
39	chr19:38635000-38642800	Weak transcription	Right Ventricle	heart
40	chr19:38635200-38642800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:38635400-38642600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:38635400-38642800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr19:38635400-38652600	Weak transcription	Stomach Mucosa	stomach
44	chr19:38635600-38642600	Weak transcription	Fetal Brain Female	brain
45	chr19:38635600-38642800	Weak transcription	HSMMtube	muscle
46	chr19:38635800-38642800	Weak transcription	Thymus	Thymus
47	chr19:38636000-38642600	Weak transcription	Brain Germinal Matrix	brain
48	chr19:38636200-38642200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:38636400-38642600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:38636400-38642800	Weak transcription	NH-A	brain

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