Variant report

Variant	rs34410821
Chromosome Location	chr19:38007105-38007106
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	chr19:37997834..37999595-chr19:38006917..38010053,3	MCF-7	breast:
2	chr19:38002449..38004595-chr19:38006976..38008761,2	K562	blood:

Variant related genes	Relation type
ENSG00000266916	Chromatin interaction
ENSG00000188227	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1019494	0.91[ASN][1000 genomes]
rs10419281	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083423	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666708	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462546	0.90[ASN][1000 genomes]
rs12981359	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981830	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545755	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1968251	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385180	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385181	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35470250	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35864326	0.84[EUR][1000 genomes]
rs4344867	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508721	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508725	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7247090	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254009	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109103	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34410821	AC012309.5	cis	Artery Tibial	GTEx
rs34410821	AC012309.5	cis	Thyroid	GTEx
rs34410821	AC012309.5	cis	Heart Left Ventricle	GTEx
rs34410821	AC012309.5	cis	Esophagus Muscularis	GTEx
rs34410821	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998600-38008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:37998800-38010800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:37998800-38014000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:37998800-38021000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:37999000-38010800	Weak transcription	Right Ventricle	heart
7	chr19:37999000-38011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:37999000-38011400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:37999000-38013800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:37999200-38008000	Weak transcription	NHEK	skin
12	chr19:37999200-38008400	Weak transcription	Fetal Heart	heart
13	chr19:37999200-38018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:37999400-38008600	Strong transcription	Brain Germinal Matrix	brain
15	chr19:37999800-38009200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:37999800-38009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:37999800-38012800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:38000200-38010400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:38000400-38008600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr19:38000800-38008800	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:38002000-38028800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:38002400-38008200	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:38002400-38009600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:38002600-38010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:38002600-38011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:38003000-38007200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:38003000-38007400	Weak transcription	Aorta	Aorta
28	chr19:38003000-38007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:38003000-38010600	Weak transcription	Fetal Muscle Leg	muscle
30	chr19:38003000-38011000	Weak transcription	Brain Angular Gyrus	brain
31	chr19:38003200-38011000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:38003800-38008600	ZNF genes & repeats	Liver	Liver
33	chr19:38004400-38008000	Weak transcription	Fetal Brain Female	brain
34	chr19:38004400-38010800	Weak transcription	Brain Substantia Nigra	brain
35	chr19:38004600-38009200	Weak transcription	Brain Anterior Caudate	brain
36	chr19:38004600-38009400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:38004600-38010600	Weak transcription	Fetal Lung	lung
38	chr19:38004600-38011000	Weak transcription	Fetal Brain Male	brain
39	chr19:38004800-38008400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:38004800-38008600	Weak transcription	Fetal Kidney	kidney
41	chr19:38004800-38010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:38004800-38010600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:38004800-38013400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:38004800-38013400	Weak transcription	Placenta	Placenta
45	chr19:38005400-38008400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:38005600-38010800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:38005600-38011000	Weak transcription	Gastric	stomach
48	chr19:38005600-38011600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:38005800-38010600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:38006000-38008000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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