Variant report

Variant	rs1654341
Chromosome Location	chr19:38540746-38540747
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	chr19:38535066..38537554-chr19:38539866..38542740,2	MCF-7	breast:
2	chr19:38540614..38543298-chr19:38547451..38549328,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10413751	0.91[EUR][1000 genomes]
rs10414433	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654343	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654347	0.92[EUR][1000 genomes]
rs1654349	0.91[EUR][1000 genomes]
rs1654350	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1654352	0.91[EUR][1000 genomes]
rs1725458	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725462	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725470	0.91[EUR][1000 genomes]
rs1725475	0.92[EUR][1000 genomes]
rs1725476	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1725507	0.91[EUR][1000 genomes]
rs1725508	0.92[EUR][1000 genomes]
rs1725509	0.91[EUR][1000 genomes]
rs1725510	0.91[EUR][1000 genomes]
rs28587798	0.82[EUR][1000 genomes]
rs57585457	0.91[EUR][1000 genomes]
rs57999412	0.91[EUR][1000 genomes]
rs7257303	0.91[EUR][1000 genomes]
rs734365	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs855597	0.81[EUR][1000 genomes]
rs855598	0.82[EUR][1000 genomes]
rs855599	0.82[EUR][1000 genomes]
rs855600	0.82[EUR][1000 genomes]
rs855601	0.82[EUR][1000 genomes]
rs855605	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs855636	0.92[EUR][1000 genomes]
rs855637	0.92[EUR][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	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
4	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
5	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
7	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
9	chr19:38531400-38550800	Weak transcription	NHLF	lung
10	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
12	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
14	chr19:38536200-38540800	Enhancers	Fetal Thymus	thymus
15	chr19:38536200-38543400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr19:38537800-38545400	Weak transcription	Fetal Stomach	stomach
17	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
19	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:38538400-38543400	Weak transcription	Fetal Intestine Large	intestine
21	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:38538600-38543200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:38539000-38545200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:38539000-38545400	Weak transcription	Gastric	stomach
25	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
26	chr19:38539200-38543000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:38539200-38545200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:38539200-38545200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:38539200-38545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:38539200-38545400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:38539200-38548800	Weak transcription	Colonic Mucosa	Colon
32	chr19:38539200-38548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
34	chr19:38539400-38540800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr19:38539600-38545400	Weak transcription	HSMM	muscle
36	chr19:38540000-38540800	Flanking Active TSS	GM12878-XiMat	blood
37	chr19:38540200-38540800	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:38540200-38540800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr19:38540200-38540800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:38540200-38541000	Enhancers	Primary T cells from cord blood	blood
41	chr19:38540200-38541000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr19:38540200-38541200	Enhancers	Primary B cells from peripheral blood	blood
43	chr19:38540200-38545200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:38540200-38545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:38540200-38545400	Weak transcription	Fetal Lung	lung
46	chr19:38540200-38545400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr19:38540200-38545400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:38540200-38548600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:38540400-38540800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr19:38540400-38540800	Enhancers	Primary T helper cells PMA-I stimulated	--

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