Variant report

Variant	rs833905
Chromosome Location	chr19:38485224-38485225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38478199..38481086-chr19:38483839..38485843,2	K562	blood:
2	chr19:38483729..38485746-chr19:38492627..38494202,2	MCF-7	breast:
3	chr19:38393241..38399415-chr19:38476540..38485383,15	MCF-7	breast:
4	chr19:38485116..38487856-chr19:38494383..38496090,2	K562	blood:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10853715	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622543	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1643455	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]
rs1643456	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643457	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1643459	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17248670	1.00[CHB][hapmap]
rs17249336	1.00[CHB][hapmap]
rs1725501	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725503	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3859549	1.00[CHB][hapmap]
rs4536583	1.00[CHB][hapmap]
rs57733318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508755	1.00[CHB][hapmap]
rs705501	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705502	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7343065	1.00[CHB][hapmap]
rs8100199	1.00[CHB][hapmap]
rs833893	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs833894	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833901	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs833902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs833903	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833906	0.85[EUR][1000 genomes]
rs833907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833908	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833919	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833920	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833921	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs833905	TMEM145	cis	cerebellum	SCAN
rs833905	ERCC2	cis	cerebellum	SCAN
rs833905	PAF1	cis	parietal	SCAN
rs833905	AKT2	cis	cerebellum	SCAN
rs833905	ZNF235	cis	cerebellum	SCAN
rs833905	ERCC2	cis	parietal	SCAN
rs833905	LYPD3	cis	parietal	SCAN
rs833905	C19orf47	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
4	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:38471400-38488600	Weak transcription	NHLF	lung
6	chr19:38472400-38493800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:38472800-38489600	Weak transcription	Fetal Kidney	kidney
8	chr19:38473200-38488600	Weak transcription	HSMMtube	muscle
9	chr19:38474800-38513600	Weak transcription	Gastric	stomach
10	chr19:38475000-38488600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:38475800-38488600	Weak transcription	Hela-S3	cervix
12	chr19:38477200-38488800	Weak transcription	Brain Anterior Caudate	brain
13	chr19:38477400-38491800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr19:38477600-38493800	Weak transcription	Thymus	Thymus
15	chr19:38479200-38493800	Weak transcription	Colonic Mucosa	Colon
16	chr19:38479600-38485400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38479800-38488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:38479800-38489800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:38480000-38485400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38480000-38488600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:38480000-38493600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:38480000-38493600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:38480000-38493800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:38480200-38489800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:38481000-38493800	Weak transcription	Small Intestine	intestine
26	chr19:38482200-38493800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:38482400-38488400	Weak transcription	Fetal Muscle Leg	muscle
28	chr19:38482400-38489200	Weak transcription	Adipose Nuclei	Adipose
29	chr19:38482400-38489600	Weak transcription	Psoas Muscle	Psoas
30	chr19:38482400-38490600	Strong transcription	Fetal Intestine Small	intestine
31	chr19:38482400-38493600	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:38482400-38493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:38482400-38493800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:38482600-38488600	Weak transcription	Brain Angular Gyrus	brain
35	chr19:38482600-38493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr19:38482600-38494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:38482600-38494000	Weak transcription	Esophagus	oesophagus
38	chr19:38482800-38485400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:38482800-38485400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:38482800-38487600	Weak transcription	NHDF-Ad	bronchial
41	chr19:38482800-38489200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr19:38482800-38490200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:38482800-38493000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:38482800-38493400	Weak transcription	Stomach Mucosa	stomach
45	chr19:38483000-38487800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr19:38483000-38488400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:38483000-38488400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:38483000-38488600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:38483000-38488600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:38483000-38493600	Weak transcription	Brain Cingulate Gyrus	brain

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