Variant report

Variant	rs34510373
Chromosome Location	chr4:57331936-57331937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57331245-57334046	U87	brain:	n/a	n/a
2	POLR2A	chr4:57331614-57332218	HCT-116	colon:	n/a	n/a
3	POLR2A	chr4:57331687-57332520	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:57331562-57334533	K562	blood:	n/a	n/a
5	GATA3	chr4:57331653-57332018	T-47D	breast:	n/a	n/a
6	SMC3	chr4:57331762-57332402	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
8	CEBPB	chr4:57331694-57332013	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:57331789-57334515	K562	blood:	n/a	n/a
10	GATA2	chr4:57331821-57332908	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr4:57329051-57334155	U87	brain:	n/a	n/a
12	POLR2A	chr4:57331630-57332358	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:57331455-57334496	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr4:57329789-57332333	U87	brain:	n/a	n/a
16	POLR2A	chr4:57331299-57334736	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr4:57331520-57332370	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr4:57331814-57334536	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr4:57331390-57332285	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:57331693-57334461	IMR90	lung:	n/a	n/a
21	POLR2A	chr4:57329197-57334826	HepG2	liver:	n/a	n/a
22	GATA3	chr4:57331585-57332013	T-47D	breast:	n/a	n/a
23	POLR2A	chr4:57331547-57332277	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr4:57331405-57334615	HepG2	liver:	n/a	n/a
25	FOXA1	chr4:57331764-57331992	T-47D	breast:	n/a	n/a
26	POLR2A	chr4:57331275-57334493	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr4:57331693-57332320	GM12891	blood:	n/a	n/a
28	ZKSCAN1	chr4:57331717-57331991	Hela-S3	cervix:	n/a	n/a
29	TBL1XR1	chr4:57331722-57331987	K562	blood:	n/a	n/a
30	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
31	MXI1	chr4:57331936-57331949	K562	blood:	n/a	n/a
32	POLR2A	chr4:57331349-57334520	K562	blood:	n/a	n/a
33	POLR2A	chr4:57331654-57332537	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr4:57331394-57334457	K562	blood:	n/a	n/a
35	MXI1	chr4:57331555-57335556	SK-N-SH	brain:	n/a	chr4:57334126-57334135
36	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
37	POLR2A	chr4:57331618-57331989	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:57331532-57332217	HCT-116	colon:	n/a	n/a
39	POLR2A	chr4:57331404-57332442	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:57331799-57332446	GM12892	blood:	n/a	n/a
41	RCOR1	chr4:57331613-57332001	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
43	TEAD4	chr4:57331618-57332021	H1-hESC	embryonic stem cell:	n/a	chr4:57331817-57331826
44	ZNF384	chr4:57331880-57333884	K562	blood:	n/a	n/a
45	POLR2A	chr4:57331525-57332047	GM12892	blood:	n/a	n/a
46	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:57331792-57332177	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr4:57331896-57334479	K562	blood:	n/a	n/a
49	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
50	JUND	chr4:57331867-57334005	K562	blood:	n/a	chr4:57332778-57332789

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57331783..57334990-chr4:57394745..57398997,7	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
4	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPAT-1	chr4:57327536-57333761	NONHSAT096505

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10010544	0.86[ASN][1000 genomes]
rs11133443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645138	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2271925	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796548	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3822001	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4565139	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56066795	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56356367	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56672277	0.90[ASN][1000 genomes]
rs59997251	0.82[ASN][1000 genomes]
rs60104031	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67343558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67721941	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836118	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6853418	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73167398	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7696808	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34510373	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
2	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57326400-57332000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:57326600-57332200	Weak transcription	Colonic Mucosa	Colon
5	chr4:57327400-57332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:57328800-57332000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:57328800-57332200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:57328800-57332800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:57330000-57332200	Enhancers	Right Ventricle	heart
10	chr4:57330200-57332200	Enhancers	Fetal Heart	heart
11	chr4:57330200-57332200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr4:57330200-57332800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:57330600-57332000	Enhancers	Colon Smooth Muscle	Colon
14	chr4:57330600-57332000	Enhancers	Rectal Smooth Muscle	rectum
15	chr4:57330800-57332000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:57330800-57332000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:57330800-57332000	Enhancers	Fetal Intestine Small	intestine
18	chr4:57330800-57332000	Enhancers	HepG2	liver
19	chr4:57330800-57332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:57330800-57332200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:57330800-57332200	Enhancers	Brain Substantia Nigra	brain
22	chr4:57330800-57332800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:57330800-57333000	Enhancers	Spleen	Spleen
24	chr4:57331000-57332200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr4:57331000-57332600	Enhancers	Stomach Mucosa	stomach
26	chr4:57331200-57332000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr4:57331200-57332200	Flanking Active TSS	K562	blood
28	chr4:57331400-57332000	Enhancers	Fetal Kidney	kidney
29	chr4:57331400-57332200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:57331400-57332200	Enhancers	Left Ventricle	heart
31	chr4:57331400-57332600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:57331400-57332600	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:57331400-57332600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:57331400-57332600	Flanking Active TSS	NHEK	skin
35	chr4:57331400-57332800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr4:57331400-57332800	Enhancers	Primary B cells from peripheral blood	blood
37	chr4:57331400-57334800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr4:57331600-57332000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr4:57331600-57332000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr4:57331600-57332000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr4:57331600-57332000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:57331600-57332000	Active TSS	Psoas Muscle	Psoas
43	chr4:57331600-57332000	Enhancers	Thymus	Thymus
44	chr4:57331600-57332200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:57331600-57332200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr4:57331600-57332400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:57331600-57332400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:57331600-57332400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr4:57331600-57332400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:57331600-57332400	Enhancers	Liver	Liver

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