Variant report

Variant	rs15740
Chromosome Location	chr1:151040435-151040436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151040279-151040435	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151040405-151040455	PrEC	prostate:	n/a
2	chr1:151040405-151040455	HRE	kidney:	n/a
3	chr1:151040405-151040455	NHDF-neo	bronchial:	n/a
4	chr1:151040405-151040455	U87	brain:	n/a
5	chr1:151040405-151040455	BJ	skin:	n/a
6	chr1:151040405-151040455	MCF-7	breast:	n/a
7	chr1:151040405-151040455	PANC-1	pancreas:	n/a
8	chr1:151040405-151040455	HPAEpiC	pulmonary alveolar:	n/a
9	chr1:151040405-151040455	GM12892	blood:	n/a
10	chr1:151040405-151040455	Hepatocyte	liver:	n/a
11	chr1:151040405-151040455	SK-N-SH	brain:	n/a
12	chr1:151040405-151040455	AG09319	gingival:	n/a
13	chr1:151040405-151040455	HEK293	kidney:	embryo
14	chr1:151040405-151040455	NHBE	bronchial:	n/a
15	chr1:151040405-151040455	Caco-2	colon:	n/a
16	chr1:151040405-151040455	CMK	blood:	n/a
17	chr1:151040405-151040455	HCPEpiC	choroid plexus:	n/a
18	chr1:151040405-151040455	SK-N-SH_RA	brain:	n/a
19	chr1:151040405-151040455	AoSMC	blood vessel:	n/a
20	chr1:151040405-151040455	HL-60	blood:	n/a
21	chr1:151040405-151040455	Hela-S3	cervix:	n/a
22	chr1:151040405-151040455	PFSK-1	brain:	n/a
23	chr1:151040405-151040455	HCM	heart:	n/a
24	chr1:151040405-151040455	NT2-D1	testis:	n/a
25	chr1:151040405-151040455	HCF	heart:	n/a
26	chr1:151040405-151040455	HEEpiC	esophagus:	n/a
27	chr1:151040405-151040455	H1-hESC	embryonic stem cell:	embryo
28	chr1:151040405-151040455	A549	lung:	n/a
29	chr1:151040405-151040455	T-47D	breast:	n/a
30	chr1:151040405-151040455	HRPEpiC	eye:	n/a
31	chr1:151040405-151040455	AG04449	skin:	fetal
32	chr1:151040405-151040455	HRCEpiC	kidney:	n/a
33	chr1:151040405-151040455	LNCaP	prostate:	n/a
34	chr1:151040405-151040455	AG04450	lung:	fetal
35	chr1:151040405-151040455	K562	blood:	n/a
36	chr1:151040405-151040455	HepG2	liver:	n/a
37	chr1:151040405-151040455	HAEpiC	amniotic membrane:	n/a
38	chr1:151040405-151040455	AG10803	skin:	n/a
39	chr1:151040405-151040455	IMR90	lung:	fetal
40	chr1:151040405-151040455	GM19239	blood:	n/a
41	chr1:151040405-151040455	HNPCEpiC	eye:	n/a
42	chr1:151040405-151040455	SAEC	small airway:	n/a
43	chr1:151040405-151040455	ovcar-3	ovarian:	n/a
44	chr1:151040405-151040455	SK-N-MC	brain:	n/a
45	chr1:151040405-151040455	HUVEC	blood vessel:	n/a
46	chr1:151040405-151040455	NB4	blood:	n/a
47	chr1:151040405-151040455	RPTEC	kidney:	n/a
48	chr1:151040405-151040455	ProgFib	skin:	n/a
49	chr1:151040405-151040455	GM12878	blood:	n/a
50	chr1:151040405-151040455	HMEC	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
2	chr1:151040243..151042047-chr1:151118960..151121134,2	MCF-7	breast:
3	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:

No data

Variant related genes	Relation type
GABPB2	TF binding region
GABPB2	CpG island
ENSG00000143412	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10749659	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788797	0.89[CHB][hapmap]
rs10788798	0.84[CEU][hapmap]
rs11204771	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11204777	0.84[CEU][hapmap]
rs11204779	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204780	0.84[CEU][hapmap]
rs12049116	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12093562	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12134957	0.84[ASN][1000 genomes]
rs12569193	0.84[GIH][hapmap]
rs1524773	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2091219	0.82[CHB][hapmap];0.85[GIH][hapmap]
rs2140709	0.84[CEU][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs2864700	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs2902811	0.83[AMR][1000 genomes]
rs3738481	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4357530	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap]
rs4970936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4970939	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4970940	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4970941	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap]
rs4970991	0.82[CHB][hapmap]
rs4970993	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4970997	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4971005	0.84[CEU][hapmap]
rs4971007	0.84[CEU][hapmap]
rs4971008	0.95[CEU][hapmap]
rs6587552	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6656450	1.00[CHB][hapmap]
rs6676190	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs6691701	0.82[CHB][hapmap]
rs6697617	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6704195	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7514185	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs15740	GABPB2	cis	cerebellum	SCAN
rs15740	PGLYRP4	cis	parietal	SCAN
rs15740	CDC42SE1	cis	Lymphoblastoid	GTEx
rs15740	MRPS21	cis	cerebellum	SCAN
rs15740	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs15740	CDC42SE1	cis	parietal	SCAN
rs15740	CDC42SE1	cis	lymphoblastoid	seeQTL
rs15740	ZNF687	cis	cerebellum	SCAN
rs15740	BNIPL	cis	lung	GTEx
rs15740	MRPS21	cis	parietal	SCAN
rs15740	CDC42SE1	cis	multi-tissue	Pritchard
rs15740	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs15740	PRPF3	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151033000-151042800	Weak transcription	Gastric	stomach
2	chr1:151033200-151042200	Weak transcription	Esophagus	oesophagus
3	chr1:151033200-151042200	Weak transcription	Pancreas	Pancrea
4	chr1:151033200-151042600	Weak transcription	Aorta	Aorta
5	chr1:151033600-151041800	Weak transcription	Primary B cells from cord blood	blood
6	chr1:151033600-151042200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:151033800-151042600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151033800-151042600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:151033800-151042600	Weak transcription	Right Atrium	heart
10	chr1:151034000-151041800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:151034000-151041800	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:151034000-151041800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:151034000-151042000	Weak transcription	Spleen	Spleen
14	chr1:151034000-151042200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:151034000-151042400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:151034200-151041600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:151034200-151042400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:151034400-151041400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:151034400-151042200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:151034600-151041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:151034600-151042600	Weak transcription	Fetal Kidney	kidney
22	chr1:151035200-151041600	Strong transcription	Fetal Thymus	thymus
23	chr1:151035800-151041800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:151035800-151041800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:151035800-151041800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151035800-151042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:151035800-151042200	Weak transcription	HMEC	breast
28	chr1:151035800-151042600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:151035800-151042600	Weak transcription	Brain Anterior Caudate	brain
30	chr1:151035800-151042600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:151035800-151042600	Weak transcription	NHEK	skin
32	chr1:151036000-151041800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:151036400-151041400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:151036400-151041800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:151036400-151042600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:151036400-151042600	Weak transcription	Osteobl	bone
37	chr1:151037200-151041600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:151037200-151041600	Weak transcription	Fetal Heart	heart
39	chr1:151037200-151042600	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:151037200-151042800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:151037400-151041000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:151037400-151041200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:151037400-151041600	Weak transcription	HSMM	muscle
44	chr1:151037400-151041800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:151037400-151042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:151037400-151042600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:151037400-151042600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:151037400-151042600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:151037600-151041800	Strong transcription	HUVEC	blood vessel
50	chr1:151037600-151042800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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