Variant report

Variant	rs1643470
Chromosome Location	chr19:38456823-38456824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
2	chr19:38455932..38458635-chr19:38458979..38461344,2	MCF-7	breast:
3	chr19:38395796..38398301-chr19:38456658..38458907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10422056	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11083438	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11083439	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11668384	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12462485	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12610891	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1632177	1.00[AFR][1000 genomes];0.87[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]
rs1643472	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725468	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1725486	0.95[ASN][1000 genomes]
rs1725490	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs241937	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs241940	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs241941	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs241942	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs241943	0.83[EUR][1000 genomes]
rs241944	0.83[EUR][1000 genomes]
rs241946	0.83[EUR][1000 genomes]
rs241948	1.00[CHB][hapmap]
rs241951	0.90[CHB][hapmap]
rs353405	0.96[EUR][1000 genomes]
rs353406	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353409	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353412	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353413	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894129	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802134	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4803536	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803566	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508748	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6508752	0.94[EUR][1000 genomes]
rs697433	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.83[AMR][1000 genomes]
rs7255551	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8102871	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8103882	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8105694	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8110417	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs833915	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833916	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs856302	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[MKK][hapmap]
rs856309	0.83[EUR][1000 genomes]
rs861308	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:38453200-38457800	Genic enhancers	A549	lung
3	chr19:38454000-38458000	Weak transcription	Small Intestine	intestine
4	chr19:38454200-38457200	Weak transcription	Lung	lung
5	chr19:38454400-38457000	Weak transcription	Stomach Mucosa	stomach
6	chr19:38454400-38460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:38454400-38461200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr19:38454600-38460800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr19:38454600-38461000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:38454800-38457000	Weak transcription	NHDF-Ad	bronchial
11	chr19:38454800-38459200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:38454800-38459200	Weak transcription	NHLF	lung
13	chr19:38455000-38457000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:38455200-38457000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:38455200-38459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38455200-38461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:38455400-38457000	Weak transcription	Osteobl	bone
18	chr19:38455600-38457000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:38456000-38461000	Weak transcription	Fetal Stomach	stomach
20	chr19:38456200-38459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr19:38456400-38457000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:38456400-38457000	Enhancers	NHEK	skin
23	chr19:38456400-38457200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr19:38456400-38457200	Enhancers	HSMMtube	muscle
25	chr19:38456400-38457400	Genic enhancers	GM12878-XiMat	blood
26	chr19:38456400-38457600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr19:38456400-38457600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:38456400-38457800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:38456400-38457800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:38456400-38457800	Enhancers	Brain Substantia Nigra	brain
31	chr19:38456400-38457800	Enhancers	Duodenum Mucosa	Duodenum
32	chr19:38456400-38457800	Enhancers	Placenta	Placenta
33	chr19:38456400-38457800	Enhancers	NH-A	brain
34	chr19:38456400-38458000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:38456400-38458200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:38456400-38458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:38456400-38459200	Genic enhancers	Fetal Intestine Small	intestine
38	chr19:38456600-38457400	Strong transcription	Primary B cells from cord blood	blood
39	chr19:38456600-38457600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr19:38456600-38457600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:38456600-38457800	Strong transcription	Primary T cells from cord blood	blood
42	chr19:38456600-38457800	Enhancers	Brain Hippocampus Middle	brain
43	chr19:38456600-38458000	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr19:38456600-38458000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:38456600-38458000	Enhancers	Fetal Intestine Large	intestine
46	chr19:38456600-38460800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:38456800-38457000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:38456800-38457000	Enhancers	Esophagus	oesophagus
49	chr19:38456800-38457200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr19:38456800-38457200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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