Variant report

Variant	rs353406
Chromosome Location	chr19:38445328-38445329
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38443941..38445562-chr19:38447183..38449175,2	MCF-7	breast:
2	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10422056	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11083438	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11083439	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11665877	0.81[AMR][1000 genomes]
rs11668384	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11668434	0.81[AMR][1000 genomes]
rs12462485	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12610891	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12972712	0.81[AMR][1000 genomes]
rs12981237	0.81[AMR][1000 genomes]
rs1632177	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643464	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643465	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643472	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725468	0.85[EUR][1000 genomes]
rs1725486	0.95[ASN][1000 genomes]
rs1725490	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17306508	0.81[AMR][1000 genomes]
rs17306795	0.91[CHB][hapmap]
rs241937	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241940	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241941	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241942	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241943	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241944	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241946	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241948	1.00[CHB][hapmap]
rs241951	0.90[CHB][hapmap]
rs34607899	0.81[AMR][1000 genomes]
rs35015599	0.81[AMR][1000 genomes]
rs35214625	0.81[AMR][1000 genomes]
rs353405	0.96[EUR][1000 genomes]
rs353409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353412	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353413	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36020184	0.81[AMR][1000 genomes]
rs36092052	0.81[AMR][1000 genomes]
rs3752365	0.81[AMR][1000 genomes]
rs3894129	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4482404	0.81[AMR][1000 genomes]
rs4802134	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803536	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803566	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508748	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6508752	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs697433	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7254828	1.00[CHB][hapmap]
rs7255551	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8102871	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8103882	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8105694	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8110417	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833915	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833916	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs856302	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs856309	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs861308	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
2	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:38426600-38450800	Weak transcription	Ovary	ovary
4	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
5	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
6	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
7	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:38439600-38453000	Weak transcription	Gastric	stomach
9	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
11	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:38441800-38445600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr19:38442000-38445600	Enhancers	GM12878-XiMat	blood
16	chr19:38442000-38445800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:38442400-38445400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr19:38443000-38447800	Weak transcription	Stomach Mucosa	stomach
19	chr19:38443400-38445400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr19:38443400-38445400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:38443400-38445600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38443600-38445800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:38443800-38445400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr19:38443800-38445400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr19:38443800-38445400	Enhancers	Fetal Kidney	kidney
26	chr19:38443800-38445600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr19:38443800-38445600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:38443800-38445600	Enhancers	Fetal Intestine Large	intestine
29	chr19:38444000-38445400	Enhancers	Fetal Intestine Small	intestine
30	chr19:38444000-38446400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
32	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38444400-38445400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr19:38444400-38445600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:38444400-38446600	Weak transcription	Psoas Muscle	Psoas
36	chr19:38444600-38446200	Weak transcription	NHEK	skin
37	chr19:38444600-38446400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:38444600-38446400	Weak transcription	HMEC	breast
39	chr19:38444600-38446600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:38444600-38450000	Weak transcription	NHDF-Ad	bronchial
41	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
43	chr19:38445000-38445400	Enhancers	Lung	lung
44	chr19:38445000-38445400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr19:38445000-38445600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:38445000-38445600	Enhancers	Primary hematopoietic stem cells	blood
47	chr19:38445000-38445600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr19:38445200-38445400	Genic enhancers	A549	lung
49	chr19:38445200-38446200	Weak transcription	Brain Anterior Caudate	brain
50	chr19:38445200-38446400	Enhancers	Fetal Heart	heart

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