Variant report

Variant	rs2304115
Chromosome Location	chr19:39421704-39421705
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	TAF1	chr19:39421168-39421815	GM12892	blood:	n/a	n/a
2	PBX3	chr19:39420821-39421901	SK-N-SH	brain:	n/a	chr19:39421459-39421468
3	POLR2A	chr19:39421161-39421797	HepG2	liver:	n/a	n/a
4	ELF1	chr19:39420661-39422148	A549	lung:	n/a	n/a
5	MXI1	chr19:39420724-39422170	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:39420743-39421919	U87	brain:	n/a	n/a
7	SP2	chr19:39421065-39421733	H1-hESC	embryonic stem cell:	n/a	chr19:39421459-39421469 chr19:39421522-39421537
8	NRF1	chr19:39420611-39422157	SK-N-SH	brain:	n/a	chr19:39421093-39421107 chr19:39421090-39421104 chr19:39421073-39421084 chr19:39421092-39421103 chr19:39421093-39421104
9	YY1	chr19:39420699-39421723	ECC-1	luminal epithelium:	n/a	chr19:39421087-39421101
10	GABPA	chr19:39420693-39422203	A549	lung:	n/a	chr19:39421093-39421107 chr19:39421090-39421104 chr19:39421093-39421104
11	TEAD4	chr19:39420548-39422095	K562	blood:	n/a	n/a
12	PML	chr19:39421065-39421838	GM12878	blood:	n/a	n/a
13	MAX	chr19:39420755-39421949	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr19:39420880-39422081	Hela-S3	cervix:	n/a	n/a
15	GABPA	chr19:39421295-39421735	K562	blood:	n/a	n/a
16	STAT1	chr19:39420743-39421762	GM12878	blood:	n/a	chr19:39421007-39421015 chr19:39420788-39420800
17	ZNF263	chr19:39420732-39421966	HEK293-T-REx	kidney:	n/a	n/a
18	RUNX3	chr19:39420565-39422173	GM12878	blood:	n/a	chr19:39420776-39420785
19	MAX	chr19:39420672-39421788	K562	blood:	n/a	n/a
20	CHD2	chr19:39420795-39421795	H1-hESC	embryonic stem cell:	n/a	n/a
21	CREB1	chr19:39420643-39421891	HepG2	liver:	n/a	n/a
22	HEY1	chr19:39420865-39421947	HepG2	liver:	n/a	chr19:39421082-39421097
23	MYC	chr19:39420783-39421830	NB4	blood:	n/a	n/a
24	TAF1	chr19:39420621-39421997	H1-hESC	embryonic stem cell:	n/a	n/a
25	HDAC2	chr19:39421489-39421744	K562	blood:	n/a	n/a
26	SP1	chr19:39420825-39421755	GM12878	blood:	n/a	chr19:39421403-39421415 chr19:39421403-39421415 chr19:39421457-39421478 chr19:39421403-39421414
27	CTCF	chr19:39419973-39422967	A549	lung:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
28	MYC	chr19:39420797-39421871	Hela-S3	cervix:	n/a	n/a
29	REST	chr19:39420945-39421929	HL-60	blood:	n/a	n/a
30	E2F4	chr19:39420999-39421709	MCF10A-Er-Src	breast:	n/a	chr19:39421094-39421103 chr19:39421458-39421467
31	POLR2A	chr19:39421117-39421872	IMR90	lung:	n/a	n/a
32	ZNF143	chr19:39420791-39421830	H1-hESC	embryonic stem cell:	n/a	chr19:39421090-39421100
33	CREB1	chr19:39420814-39421938	K562	blood:	n/a	n/a
34	RCOR1	chr19:39421635-39422052	K562	blood:	n/a	n/a
35	SP2	chr19:39421085-39421809	HepG2	liver:	n/a	chr19:39421459-39421469 chr19:39421522-39421537
36	POLR2A	chr19:39420786-39422005	MCF10A-Er-Src	breast:	n/a	n/a
37	CREB1	chr19:39421006-39421917	ECC-1	luminal epithelium:	n/a	n/a
38	TBP	chr19:39420860-39421881	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr19:39421101-39421798	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:39420837-39421874	HUVEC	blood vessel:	n/a	n/a
41	SIN3AK20	chr19:39420531-39422245	MCF-7	breast:	n/a	n/a
42	SIN3AK20	chr19:39420376-39422495	A549	lung:	n/a	n/a
43	CTCF	chr19:39420176-39422260	SK-N-SH	brain:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
44	TAF1	chr19:39420853-39421857	H1-hESC	embryonic stem cell:	n/a	n/a
45	TCF12	chr19:39420763-39421813	ECC-1	luminal epithelium:	n/a	n/a
46	SMARCC1	chr19:39420815-39422012	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr19:39420660-39422526	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr19:39420932-39421864	GM18526	blood:	n/a	n/a
49	CHD1	chr19:39420736-39422193	GM12878	blood:	n/a	n/a
50	CREB1	chr19:39420579-39421861	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39420462..39423214-chr19:39898290..39900735,2	K562	blood:
2	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
3	chr19:39398838..39403067-chr19:39419638..39422578,4	MCF-7	breast:
4	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
5	chr19:39420986..39421850-chr9:138392329..138393182,2	Hela-S3	cervix:
6	chr19:39420991..39421729-chr5:41870292..41870960,2	Hela-S3	cervix:
7	chr19:39420846..39421801-chr7:150065013..150066008,2	HCT-116	colon:
8	chr14:24898542..24899536-chr19:39421414..39422162,2	HCT-116	colon:
9	chr19:39322407..39324148-chr19:39419876..39421918,2	K562	blood:
10	chr19:39421083..39425618-chr19:39435632..39441753,7	MCF-7	breast:
11	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
12	chr19:39326367..39329872-chr19:39419342..39422625,3	MCF-7	breast:
13	chr19:39388885..39392214-chr19:39419332..39422757,5	MCF-7	breast:
14	chr19:39358835..39360669-chr19:39419879..39421985,2	K562	blood:
15	chr19:39411897..39413585-chr19:39419804..39422534,2	K562	blood:
16	chr19:39389410..39392783-chr19:39420988..39423307,4	MCF-7	breast:
17	chr1:109642705..109643242-chr19:39421269..39422117,2	Hela-S3	cervix:
18	chr19:39420323..39422094-chr19:39898290..39901814,3	K562	blood:
19	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
20	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
21	chr13:52026821..52027491-chr19:39421527..39422118,2	HCT-116	colon:
22	chr19:39228667..39230478-chr19:39420914..39423370,2	MCF-7	breast:
23	chr19:39420306..39422739-chr19:39440304..39443002,2	K562	blood:
24	chr19:39411214..39414705-chr19:39419221..39421908,4	MCF-7	breast:
25	chr19:39370268..39372714-chr19:39419858..39422598,3	K562	blood:
26	chr19:39421489..39422117-chr2:113239290..113239831,2	Hela-S3	cervix:

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000262484	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000270066	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000122140	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000269190	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000160345	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000269547	Chromatin interaction
ENSG00000187994	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10411209	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423309	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083487	1.00[JPT][hapmap]
rs13343573	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972885	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2070250	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082436	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2116853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163811	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304116	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362605	1.00[ASN][1000 genomes]
rs28808414	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28824318	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28844707	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28860185	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3181068	1.00[ASN][1000 genomes]
rs34264048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58399999	1.00[ASN][1000 genomes]
rs61194027	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61232096	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508826	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508827	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73537679	1.00[ASN][1000 genomes]
rs73930228	0.84[AMR][1000 genomes]
rs73930229	0.84[AMR][1000 genomes]
rs8113749	0.85[AMR][1000 genomes];1.00[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2304115	MRPS12	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39420000-39422600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:39420200-39422400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39420200-39422600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:39420200-39422600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:39420200-39422600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:39420200-39422600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:39420200-39422600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:39420400-39422400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr19:39420400-39422400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:39420400-39422600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:39420400-39422600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39420400-39422600	Active TSS	HSMM	muscle
13	chr19:39420400-39422600	Active TSS	HSMMtube	muscle
14	chr19:39420400-39422600	Active TSS	K562	blood
15	chr19:39420600-39422000	Active TSS	Lung	lung
16	chr19:39420600-39422200	Active TSS	Ovary	ovary
17	chr19:39420600-39422200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr19:39420600-39422400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39420600-39422400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:39420600-39422400	Active TSS	Esophagus	oesophagus
21	chr19:39420600-39422400	Active TSS	Fetal Kidney	kidney
22	chr19:39420600-39422400	Active TSS	Gastric	stomach
23	chr19:39420600-39422400	Active TSS	Left Ventricle	heart
24	chr19:39420600-39422400	Active TSS	Psoas Muscle	Psoas
25	chr19:39420600-39422400	Active TSS	Right Atrium	heart
26	chr19:39420600-39422600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:39420600-39422600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:39420600-39422800	Active TSS	GM12878-XiMat	blood
29	chr19:39420800-39421800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39420800-39422000	Active TSS	Brain Angular Gyrus	brain
31	chr19:39420800-39422000	Active TSS	Brain Anterior Caudate	brain
32	chr19:39420800-39422000	Active TSS	Fetal Brain Male	brain
33	chr19:39420800-39422200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr19:39420800-39422200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:39420800-39422200	Active TSS	Aorta	Aorta
36	chr19:39420800-39422200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:39420800-39422200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:39420800-39422400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:39420800-39422400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:39420800-39422400	Active TSS	Fetal Heart	heart
41	chr19:39420800-39422400	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr19:39420800-39422400	Active TSS	Small Intestine	intestine
43	chr19:39420800-39422400	Active TSS	NHEK	skin
44	chr19:39420800-39422600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:39420800-39422600	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:39420800-39422800	Active TSS	A549	lung
47	chr19:39421000-39421800	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr19:39421000-39421800	Active TSS	Primary B cells from peripheral blood	blood
49	chr19:39421000-39421800	Active TSS	Primary T cells from cord blood	blood
50	chr19:39421000-39421800	Active TSS	Primary T cells fromperipheralblood	blood

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