Variant report

Variant	rs751941
Chromosome Location	chr19:39416409-39416410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39416345-39416462	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39415679..39418451-chr19:39423572..39425396,2	MCF-7	breast:
2	chr19:39416038..39418254-chr19:39423226..39425475,2	K562	blood:
3	chr19:39414900..39416436-chr19:39417401..39420305,2	K562	blood:

Variant related genes	Relation type
MRPS12	TF binding region
SARS2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10407879	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10410176	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10412886	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10415194	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134180	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11882588	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460327	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462170	0.91[ASN][1000 genomes]
rs2099339	0.95[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2116854	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2116855	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2288855	0.82[ASN][1000 genomes]
rs28375245	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3136644	0.86[GIH][hapmap]
rs3136645	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap]
rs4801945	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs751941	ATP5SL	cis	parietal	SCAN
rs751941	SARS2	cis	multi-tissue	Pritchard
rs751941	ZNF230	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
3	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
5	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:39403600-39420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:39403800-39420200	Weak transcription	Fetal Brain Male	brain
8	chr19:39406400-39420000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:39406800-39420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:39409000-39417400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:39409200-39419000	Strong transcription	Fetal Intestine Small	intestine
12	chr19:39409200-39420400	Weak transcription	Stomach Mucosa	stomach
13	chr19:39409600-39418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:39410000-39417400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:39410200-39417600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:39411400-39419000	Strong transcription	Fetal Stomach	stomach
17	chr19:39411600-39417000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:39411600-39420400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39411600-39420400	Weak transcription	Fetal Heart	heart
20	chr19:39411800-39417200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:39412000-39416600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:39412000-39417000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr19:39412000-39417200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:39412000-39417200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:39412000-39417600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:39412000-39419000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:39412000-39419600	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:39412200-39417000	Strong transcription	Right Ventricle	heart
29	chr19:39412200-39417400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:39412200-39419200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:39412400-39416600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:39412400-39417200	Strong transcription	Fetal Intestine Large	intestine
33	chr19:39412800-39420600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:39413200-39418800	Weak transcription	GM12878-XiMat	blood
35	chr19:39413200-39420200	Weak transcription	Primary B cells from cord blood	blood
36	chr19:39413200-39420200	Weak transcription	NH-A	brain
37	chr19:39413200-39420200	Weak transcription	NHLF	lung
38	chr19:39413200-39420400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr19:39413200-39420400	Weak transcription	Fetal Kidney	kidney
40	chr19:39413200-39420800	Weak transcription	Aorta	Aorta
41	chr19:39414400-39417000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:39414400-39417200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr19:39414400-39417200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr19:39414400-39417200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr19:39414400-39417200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:39414400-39417200	Strong transcription	Liver	Liver
47	chr19:39414400-39417200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr19:39414400-39417200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:39414400-39418600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:39414400-39419400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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