Variant report

Variant	rs1530290
Chromosome Location	chr5:68628252-68628253
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	MAX	chr5:68627739-68628939	NB4	blood:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
2	POLR2A	chr5:68627479-68628844	HepG2	liver:	n/a	n/a
3	USF1	chr5:68628239-68629064	SK-N-SH	brain:	n/a	chr5:68628650-68628661 chr5:68628621-68628637
4	E2F6	chr5:68628224-68629174	A549	lung:	n/a	chr5:68628615-68628624 chr5:68628626-68628636
5	RCOR1	chr5:68627735-68628862	HepG2	liver:	n/a	n/a
6	ARID3A	chr5:68627607-68628919	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:68628244-68629322	MCF-7	breast:	n/a	n/a
8	MAX	chr5:68628209-68629066	HepG2	liver:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
9	USF1	chr5:68628247-68629051	ECC-1	luminal epithelium:	n/a	chr5:68628650-68628661 chr5:68628621-68628637
10	EGR1	chr5:68628206-68629134	HCT-116	colon:	n/a	chr5:68628661-68628671 chr5:68628659-68628673 chr5:68628610-68628619 chr5:68628615-68628624 chr5:68628659-68628672
11	PML	chr5:68628005-68629115	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:68628204-68629068	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr5:68628220-68629123	A549	lung:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
14	MXI1	chr5:68628221-68628880	Hela-S3	cervix:	n/a	chr5:68628652-68628661
15	TAF1	chr5:68628217-68628988	ECC-1	luminal epithelium:	n/a	n/a
16	MYBL2	chr5:68627533-68628258	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:68628251-68629011	MCF-7	breast:	n/a	n/a
18	POLR2A	chr5:68628244-68629067	GM12878	blood:	n/a	n/a
19	TAF1	chr5:68628183-68628897	ECC-1	luminal epithelium:	n/a	n/a
20	SIN3AK20	chr5:68628212-68629071	MCF-7	breast:	n/a	n/a
21	MXI1	chr5:68628033-68629198	SK-N-SH	brain:	n/a	chr5:68628652-68628661
22	MAX	chr5:68628148-68628946	GM12878	blood:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
23	MAX	chr5:68628099-68628956	A549	lung:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
24	POLR2A	chr5:68628101-68628937	PBDE	blood:	n/a	n/a
25	POLR2A	chr5:68627608-68628920	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:68628214-68629030	GM12892	blood:	n/a	n/a
27	MXI1	chr5:68627962-68628901	GM12878	blood:	n/a	chr5:68628652-68628661
28	TBL1XR1	chr5:68628147-68628904	K562	blood:	n/a	n/a
29	ZNF263	chr5:68628188-68628903	HEK293-T-REx	kidney:	n/a	n/a
30	STAT5A	chr5:68628160-68628948	GM12878	blood:	n/a	chr5:68628415-68628429
31	USF1	chr5:68628230-68629050	HCT-116	colon:	n/a	chr5:68628650-68628661 chr5:68628621-68628637
32	GABPA	chr5:68628158-68629146	MCF-7	breast:	n/a	chr5:68628614-68628625 chr5:68628611-68628625
33	MYC	chr5:68628137-68628337	MCF10A-Er-Src	breast:	n/a	n/a
34	MAX	chr5:68628191-68629131	ECC-1	luminal epithelium:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
35	POLR2A	chr5:68627892-68629020	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:68628232-68629000	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:68627653-68628960	GM12891	blood:	n/a	n/a
38	TAF1	chr5:68628206-68628989	A549	lung:	n/a	n/a
39	HCFC1	chr5:68627600-68629135	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr5:68628214-68629063	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:68628135-68629014	PFSK-1	brain:	n/a	n/a
42	MAX	chr5:68628235-68629125	HCT-116	colon:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
43	SIN3AK20	chr5:68628199-68629072	MCF-7	breast:	n/a	n/a
44	EP300	chr5:68627802-68628842	HepG2	liver:	n/a	n/a
45	MAX	chr5:68628206-68629137	A549	lung:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
46	MAX	chr5:68628217-68629017	ECC-1	luminal epithelium:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
47	POLR2A	chr5:68628187-68629021	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr5:68627902-68628923	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr5:68628230-68629013	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:68627441-68628937	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:68628240-68628290	HIPEpiC	eye:	n/a
2	chr5:68628240-68628290	GM12892	blood:	n/a
3	chr5:68628240-68628290	HRPEpiC	eye:	n/a
4	chr5:68628240-68628290	H1-hESC	embryonic stem cell:	embryo
5	chr5:68628240-68628290	GM19239	blood:	n/a
6	chr5:68628240-68628290	ECC-1	luminal epithelium:	n/a
7	chr5:68628240-68628290	HNPCEpiC	eye:	n/a
8	chr5:68628240-68628290	K562	blood:	n/a
9	chr5:68628240-68628290	MCF10A-Er-Src	breast:	n/a
10	chr5:68628240-68628290	GM12891	blood:	n/a
11	chr5:68628240-68628290	AG10803	skin:	n/a
12	chr5:68628240-68628290	CMK	blood:	n/a
13	chr5:68628240-68628290	BE2_C	brain:	n/a
14	chr5:68628240-68628290	PFSK-1	brain:	n/a
15	chr5:68628240-68628290	AG04449	skin:	fetal
16	chr5:68628240-68628290	A549	lung:	n/a
17	chr5:68628240-68628290	Hepatocyte	liver:	n/a
18	chr5:68628240-68628290	Jurkat	blood:	n/a
19	chr5:68628240-68628290	T-47D	breast:	n/a
20	chr5:68628240-68628290	HPAEpiC	pulmonary alveolar:	n/a
21	chr5:68628240-68628290	AG09309	skin:	n/a
22	chr5:68628240-68628290	AoSMC	blood vessel:	n/a
23	chr5:68628240-68628290	HRE	kidney:	n/a
24	chr5:68628240-68628290	SK-N-MC	brain:	n/a
25	chr5:68628240-68628290	NT2-D1	testis:	n/a
26	chr5:68628240-68628290	LNCaP	prostate:	n/a
27	chr5:68628240-68628290	IMR90	lung:	fetal
28	chr5:68628240-68628290	HMEC	breast:	n/a
29	chr5:68628240-68628290	RPTEC	kidney:	n/a
30	chr5:68628240-68628290	PANC-1	pancreas:	n/a
31	chr5:68628240-68628290	HEK293	kidney:	embryo
32	chr5:68628240-68628290	HCM	heart:	n/a
33	chr5:68628240-68628290	SK-N-SH	brain:	n/a
34	chr5:68628240-68628290	SKMC	muscle:	n/a
35	chr5:68628240-68628290	HL-60	blood:	n/a
36	chr5:68628240-68628290	Caco-2	colon:	n/a
37	chr5:68628240-68628290	U87	brain:	n/a
38	chr5:68628240-68628290	HRCEpiC	kidney:	n/a
39	chr5:68628240-68628290	GM12878	blood:	n/a
40	chr5:68628240-68628290	NB4	blood:	n/a
41	chr5:68628240-68628290	NHBE	bronchial:	n/a
42	chr5:68628240-68628290	MCF-7	breast:	n/a
43	chr5:68628240-68628290	HCF	heart:	n/a
44	chr5:68628240-68628290	HEEpiC	esophagus:	n/a
45	chr5:68628240-68628290	ProgFib	skin:	n/a
46	chr5:68628240-68628290	ovcar-3	ovarian:	n/a
47	chr5:68628240-68628290	NH-A	brain:	n/a
48	chr5:68628240-68628290	Hela-S3	cervix:	n/a
49	chr5:68628240-68628290	BJ	skin:	n/a
50	chr5:68628240-68628290	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68628027..68630302-chr5:68663373..68666765,3	K562	blood:
2	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
3	chr5:68626762..68628383-chr5:68787111..68789288,2	MCF-7	breast:
4	chr5:68485299..68487066-chr5:68626120..68629033,4	MCF-7	breast:
5	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
6	chr5:68606839..68610803-chr5:68625940..68628885,4	MCF-7	breast:
7	chr5:68529975..68532202-chr5:68627120..68629377,3	MCF-7	breast:
8	chr5:68588146..68590724-chr5:68626782..68628489,2	MCF-7	breast:
9	chr5:68388706..68391393-chr5:68627238..68631529,6	MCF-7	breast:

Variant related genes	Relation type
CHCHD2P2	TF binding region
CHCHD2P2	CpG island
ENSG00000197822	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000213830	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10044508	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10045361	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10471350	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471774	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10471775	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471776	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940212	0.83[EUR][1000 genomes]
rs10940216	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940218	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12187268	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188076	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517724	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178839	0.81[EUR][1000 genomes]
rs13361598	0.82[EUR][1000 genomes]
rs2010352	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28580747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34935424	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4252228	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4473723	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976160	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4976189	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976190	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4976194	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58772585	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62373187	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6450029	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6450032	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873869	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6875069	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879078	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708429	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712318	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9291947	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291948	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791036	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1530290	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs1530290	MRPS36	cis	lymphoblastoid	seeQTL
rs1530290	CCDC125	cis	lung	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68609800-68628400	Weak transcription	Lung	lung
2	chr5:68627000-68628800	Active TSS	Duodenum Mucosa	Duodenum
3	chr5:68627200-68628400	Weak transcription	Gastric	stomach
4	chr5:68627200-68628800	Active TSS	Colonic Mucosa	Colon
5	chr5:68627200-68629200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr5:68627400-68628400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:68627400-68628800	Active TSS	Fetal Intestine Small	intestine
8	chr5:68627400-68628800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:68627400-68628800	Active TSS	Fetal Stomach	stomach
10	chr5:68627400-68628800	Flanking Active TSS	HMEC	breast
11	chr5:68627400-68629000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr5:68627400-68629000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr5:68627400-68629000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr5:68627400-68629000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr5:68627400-68629000	Flanking Active TSS	NHEK	skin
16	chr5:68627400-68629200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:68627600-68628400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr5:68627600-68628400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:68627600-68628400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr5:68627600-68628400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr5:68627600-68628400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr5:68627600-68628600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr5:68627600-68628800	Active TSS	Fetal Intestine Large	intestine
24	chr5:68627600-68628800	Active TSS	Stomach Mucosa	stomach
25	chr5:68627600-68629000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr5:68627600-68629000	Active TSS	Fetal Kidney	kidney
27	chr5:68627600-68629000	Active TSS	Thymus	Thymus
28	chr5:68627600-68629200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:68627800-68628400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr5:68627800-68628400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr5:68627800-68628400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:68627800-68628600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr5:68627800-68628600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:68627800-68628600	Active TSS	GM12878-XiMat	blood
35	chr5:68627800-68628600	Active TSS	HepG2	liver
36	chr5:68627800-68628800	Active TSS	Liver	Liver
37	chr5:68627800-68628800	Active TSS	Fetal Brain Male	brain
38	chr5:68627800-68628800	Active TSS	Pancreas	Pancrea
39	chr5:68627800-68628800	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr5:68627800-68628800	Active TSS	NHDF-Ad	bronchial
41	chr5:68627800-68628800	Active TSS	NHLF	lung
42	chr5:68627800-68628800	Active TSS	Osteobl	bone
43	chr5:68627800-68629000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr5:68627800-68629000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr5:68627800-68629000	Active TSS	Brain Hippocampus Middle	brain
46	chr5:68627800-68629000	Active TSS	Fetal Lung	lung
47	chr5:68627800-68629200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr5:68627800-68629200	Active TSS	Stomach Smooth Muscle	stomach
49	chr5:68628000-68628400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:68628000-68628400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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