Variant report

Variant	rs1538145
Chromosome Location	chr13:38445304-38445305
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr13:38445188-38445311	K562	blood:	n/a	n/a
2	MAX	chr13:38444445-38445454	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr13:38445005-38445632	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr13:38445275-38445383	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr13:38444253-38445323	HEK293	kidney:	n/a	n/a
6	TBP	chr13:38444208-38445353	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr13:38444132-38445448	H1-hESC	embryonic stem cell:	n/a	chr13:38444288-38444300
8	REST	chr13:38442575-38445418	H1-neurons	neurons:	n/a	chr13:38443382-38443396 chr13:38443882-38443900 chr13:38443384-38443394 chr13:38443403-38443411 chr13:38444081-38444094
9	RAD21	chr13:38442828-38445372	H1-hESC	embryonic stem cell:	n/a	chr13:38443893-38443905 chr13:38444288-38444300
10	GATA2	chr13:38444442-38445367	HUVEC	blood vessel:	n/a	chr13:38444875-38444891 chr13:38444874-38444888
11	SIN3A	chr13:38442773-38445714	H1-hESC	embryonic stem cell:	n/a	chr13:38443787-38443800

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:38445267-38445317	PFSK-1	brain:	n/a
2	chr13:38445267-38445317	SK-N-MC	brain:	n/a
3	chr13:38445267-38445317	SK-N-SH_RA	brain:	n/a
4	chr13:38445267-38445317	HMEC	breast:	n/a
5	chr13:38445267-38445317	ProgFib	skin:	n/a
6	chr13:38445267-38445317	AG09319	gingival:	n/a
7	chr13:38445267-38445317	AG10803	skin:	n/a
8	chr13:38445267-38445317	SAEC	small airway:	n/a
9	chr13:38445267-38445317	BJ	skin:	n/a
10	chr13:38445267-38445317	NT2-D1	testis:	n/a
11	chr13:38445267-38445317	HEK293	kidney:	embryo
12	chr13:38445267-38445317	HCM	heart:	n/a
13	chr13:38445267-38445317	GM19239	blood:	n/a
14	chr13:38445267-38445317	AG09309	skin:	n/a
15	chr13:38445267-38445317	HPAEpiC	pulmonary alveolar:	n/a
16	chr13:38445267-38445317	ECC-1	luminal epithelium:	n/a
17	chr13:38445267-38445317	AoSMC	blood vessel:	n/a
18	chr13:38445267-38445317	AG04449	skin:	fetal
19	chr13:38445267-38445317	GM06990	blood:	n/a
20	chr13:38445267-38445317	Caco-2	colon:	n/a
21	chr13:38445267-38445317	BE2_C	brain:	n/a
22	chr13:38445267-38445317	IMR90	lung:	fetal
23	chr13:38445267-38445317	NHDF-neo	bronchial:	n/a
24	chr13:38445267-38445317	HCF	heart:	n/a
25	chr13:38445267-38445317	Hepatocyte	liver:	n/a
26	chr13:38445267-38445317	HAEpiC	amniotic membrane:	n/a
27	chr13:38445267-38445317	Jurkat	blood:	n/a
28	chr13:38445267-38445317	H1-hESC	embryonic stem cell:	embryo
29	chr13:38445267-38445317	PrEC	prostate:	n/a
30	chr13:38445267-38445317	SK-N-SH	brain:	n/a
31	chr13:38445267-38445317	GM12892	blood:	n/a
32	chr13:38445267-38445317	HCT-116	colon:	n/a
33	chr13:38445267-38445317	AG04450	lung:	fetal
34	chr13:38445267-38445317	HEEpiC	esophagus:	n/a
35	chr13:38445267-38445317	MCF-7	breast:	n/a
36	chr13:38445267-38445317	HRCEpiC	kidney:	n/a
37	chr13:38445267-38445317	GM12878	blood:	n/a
38	chr13:38445267-38445317	HRE	kidney:	n/a
39	chr13:38445267-38445317	LNCaP	prostate:	n/a
40	chr13:38445267-38445317	ovcar-3	ovarian:	n/a
41	chr13:38445267-38445317	PANC-1	pancreas:	n/a
42	chr13:38445267-38445317	K562	blood:	n/a
43	chr13:38445267-38445317	NH-A	brain:	n/a
44	chr13:38445267-38445317	A549	lung:	n/a
45	chr13:38445267-38445317	NHBE	bronchial:	n/a
46	chr13:38445267-38445317	HRPEpiC	eye:	n/a
47	chr13:38445267-38445317	HNPCEpiC	eye:	n/a
48	chr13:38445267-38445317	CMK	blood:	n/a
49	chr13:38445267-38445317	MCF10A-Er-Src	breast:	n/a
50	chr13:38445267-38445317	RPTEC	kidney:	n/a

No data

Variant related genes	Relation type
TRPC4	TF binding region
TRPC4	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12431204	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1337601	0.85[ASN][1000 genomes]
rs1538146	0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs1538148	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1924379	0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs2323637	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812837	0.83[ASN][1000 genomes]
rs4144140	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548085	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548086	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548087	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548090	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9566272	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576389	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38442800-38445400	Active TSS	Brain Angular Gyrus	brain
2	chr13:38443200-38445400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:38443400-38445400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
4	chr13:38444000-38445400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr13:38444200-38445400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:38444200-38445400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr13:38444400-38445800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:38444600-38445400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:38444600-38445400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr13:38444600-38445400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:38444600-38445400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:38444600-38445400	Bivalent Enhancer	Fetal Heart	heart
13	chr13:38444600-38445400	Flanking Active TSS	NHDF-Ad	bronchial
14	chr13:38444600-38445400	Flanking Active TSS	NHLF	lung
15	chr13:38444600-38445400	Flanking Active TSS	Osteobl	bone
16	chr13:38444600-38445600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr13:38444600-38445600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:38444600-38445600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:38444600-38445600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:38444600-38445600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:38444600-38445600	Flanking Active TSS	NH-A	brain
22	chr13:38444600-38445600	Flanking Active TSS	NHEK	skin
23	chr13:38444800-38445400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:38444800-38445400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:38444800-38445400	Active TSS	Brain Anterior Caudate	brain
26	chr13:38444800-38445400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr13:38444800-38445400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
28	chr13:38444800-38445400	Bivalent Enhancer	HSMMtube	muscle
29	chr13:38444800-38445600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:38444800-38462200	Weak transcription	Pancreas	Pancrea
31	chr13:38445000-38445400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:38445000-38445400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr13:38445000-38446000	Enhancers	HSMM	muscle
34	chr13:38445000-38446400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:38445200-38445400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr13:38445200-38445400	Flanking Active TSS	Ovary	ovary
37	chr13:38445200-38445400	Flanking Active TSS	Right Atrium	heart
38	chr13:38445200-38445600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr13:38445200-38445600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
40	chr13:38445200-38445600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr13:38445200-38445800	Enhancers	HMEC	breast

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