Variant report

Variant	rs1643455
Chromosome Location	chr19:38503652-38503653
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	chr19:38397004..38399373-chr19:38501690..38504225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10853715	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1622543	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643456	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1643457	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1643459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17248670	1.00[CHB][hapmap]
rs17249336	1.00[CHB][hapmap]
rs1725501	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725503	0.95[EUR][1000 genomes]
rs2694065	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3859549	1.00[CHB][hapmap]
rs4536583	1.00[CHB][hapmap]
rs57733318	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6508755	1.00[CHB][hapmap]
rs705501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs705502	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7343065	1.00[CHB][hapmap]
rs8100199	1.00[CHB][hapmap]
rs833893	0.95[EUR][1000 genomes]
rs833894	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833901	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs833902	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs833903	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833904	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833905	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833906	0.81[EUR][1000 genomes]
rs833907	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs833908	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs833919	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833921	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38474800-38513600	Weak transcription	Gastric	stomach
2	chr19:38495400-38503800	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr19:38495400-38522800	Weak transcription	Aorta	Aorta
4	chr19:38495400-38526400	Weak transcription	Ovary	ovary
5	chr19:38495600-38509200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:38495600-38512800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr19:38495600-38513400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:38495600-38514200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:38495800-38510000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr19:38495800-38513400	Weak transcription	Stomach Mucosa	stomach
11	chr19:38496000-38505600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:38496200-38508000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:38496200-38508200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:38496200-38509400	Weak transcription	HSMMtube	muscle
15	chr19:38496200-38512600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38496200-38513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:38496200-38513600	Weak transcription	Left Ventricle	heart
18	chr19:38496200-38513600	Weak transcription	Right Ventricle	heart
19	chr19:38496200-38513600	Weak transcription	NHEK	skin
20	chr19:38496200-38521400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:38496400-38510800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:38496400-38511000	Weak transcription	Brain Germinal Matrix	brain
23	chr19:38496400-38521400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:38496600-38513600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:38496600-38515600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:38496800-38506600	Weak transcription	Osteobl	bone
27	chr19:38496800-38509400	Weak transcription	HUVEC	blood vessel
28	chr19:38496800-38520600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:38497000-38513400	Weak transcription	NHLF	lung
30	chr19:38497400-38504200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:38497400-38511800	Weak transcription	NH-A	brain
32	chr19:38497400-38515800	Weak transcription	Fetal Brain Male	brain
33	chr19:38497400-38520600	Weak transcription	Primary T cells from cord blood	blood
34	chr19:38497600-38513600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:38498200-38514800	Weak transcription	HepG2	liver
36	chr19:38500600-38524200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:38500800-38504400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr19:38501000-38521400	Weak transcription	Thymus	Thymus
39	chr19:38501400-38507400	Strong transcription	GM12878-XiMat	blood
40	chr19:38501800-38511000	Weak transcription	HSMM	muscle
41	chr19:38502000-38503800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:38502000-38503800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:38502000-38503800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:38502000-38506000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:38502200-38503800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:38502200-38503800	Genic enhancers	A549	lung
47	chr19:38502200-38504000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:38502200-38504800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:38502400-38503800	Enhancers	Lung	lung
50	chr19:38502400-38504200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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