Variant report

Variant	rs734204
Chromosome Location	chr19:38539988-38539989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38535066..38537554-chr19:38539866..38542740,2	MCF-7	breast:
2	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
3	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10414433	0.81[CHB][hapmap]
rs10421137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1616705	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1618385	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1620082	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1623976	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1628394	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654339	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654344	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654374	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725459	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725463	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725464	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725467	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725505	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725514	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725515	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725516	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725517	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725518	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5022085	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5022086	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508759	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508761	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508762	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249241	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256480	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256626	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256656	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256804	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106776	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941036	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941037	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv911656	chr19:38505037-38539988	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs734204	APOE	cis	cerebellum	SCAN
rs734204	CCDC8	cis	parietal	SCAN
rs734204	FBXO46	cis	parietal	SCAN
rs734204	ZNF229	cis	cerebellum	SCAN
rs734204	IGFL1	cis	cerebellum	SCAN
rs734204	PHLDB3	cis	parietal	SCAN
rs734204	ZNF229	cis	parietal	SCAN
rs734204	RAB4B	cis	parietal	SCAN

Chromatin state (count:82 , 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	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
5	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
6	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
8	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
10	chr19:38531400-38550800	Weak transcription	NHLF	lung
11	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
14	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:38535200-38540000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
17	chr19:38536200-38540800	Enhancers	Fetal Thymus	thymus
18	chr19:38536200-38543400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:38537800-38540400	Enhancers	Fetal Muscle Leg	muscle
20	chr19:38537800-38545400	Weak transcription	Fetal Stomach	stomach
21	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
23	chr19:38538000-38540000	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38538200-38540000	Enhancers	Fetal Muscle Trunk	muscle
26	chr19:38538200-38540200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr19:38538400-38540000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:38538400-38540200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr19:38538400-38540200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr19:38538400-38543400	Weak transcription	Fetal Intestine Large	intestine
31	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:38538600-38540000	Weak transcription	Lung	lung
33	chr19:38538600-38540400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:38538600-38540400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr19:38538600-38543200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38538800-38540400	Flanking Active TSS	Dnd41	blood
37	chr19:38538800-38540600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr19:38538800-38540600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr19:38539000-38540000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:38539000-38545200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:38539000-38545400	Weak transcription	Gastric	stomach
42	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
43	chr19:38539200-38540000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:38539200-38540200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr19:38539200-38540200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr19:38539200-38540200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:38539200-38540200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:38539200-38540400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr19:38539200-38540400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr19:38539200-38540400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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