Variant report

Variant	rs3812837
Chromosome Location	chr13:38445196-38445197
allele	A/C
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	BHLHE40	chr13:38445188-38445311	K562	blood:	n/a	n/a
2	TAL1	chr13:38444996-38445277	K562	blood:	n/a	n/a
3	MAX	chr13:38444445-38445454	H1-hESC	embryonic stem cell:	n/a	n/a
4	STAT3	chr13:38445005-38445632	MCF10A-Er-Src	breast:	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	BACH1	chr13:38444435-38445233	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr13:38444132-38445448	H1-hESC	embryonic stem cell:	n/a	chr13:38444288-38444300
9	REST	chr13:38442575-38445418	H1-neurons	neurons:	n/a	chr13:38443382-38443396 chr13:38443882-38443900 chr13:38443384-38443394 chr13:38443403-38443411 chr13:38444081-38444094
10	RAD21	chr13:38442828-38445372	H1-hESC	embryonic stem cell:	n/a	chr13:38443893-38443905 chr13:38444288-38444300
11	GATA2	chr13:38444442-38445367	HUVEC	blood vessel:	n/a	chr13:38444875-38444891 chr13:38444874-38444888
12	CTBP2	chr13:38443161-38445209	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr13:38442773-38445714	H1-hESC	embryonic stem cell:	n/a	chr13:38443787-38443800

Variant related genes	Relation type
TRPC4	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12584216	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12874874	0.91[MEX][hapmap]
rs1337601	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1415601	0.91[CEU][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1538145	0.83[ASN][1000 genomes]
rs1538146	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1538148	0.82[CHD][hapmap]
rs1577876	0.91[MEX][hapmap]
rs17272200	0.91[MEX][hapmap]
rs1819607	0.91[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap]
rs1924379	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2323637	0.83[ASN][1000 genomes]
rs2323638	0.88[ASN][1000 genomes]
rs3812840	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3812841	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4144140	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs942345	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9532131	0.93[ASW][hapmap];0.91[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9548066	0.91[MEX][hapmap]
rs9548076	0.91[MEX][hapmap]
rs9548078	0.91[MEX][hapmap]
rs9548087	0.80[ASN][1000 genomes]
rs9566272	0.82[ASN][1000 genomes]
rs9576388	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38440600-38445200	Active TSS	Fetal Brain Female	brain
2	chr13:38442200-38445200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr13:38442400-38445200	Active TSS	Ovary	ovary
4	chr13:38442800-38445200	Active TSS	Right Atrium	heart
5	chr13:38442800-38445400	Active TSS	Brain Angular Gyrus	brain
6	chr13:38443000-38445200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr13:38443200-38445400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:38443400-38445400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
9	chr13:38444000-38445200	Flanking Active TSS	HMEC	breast
10	chr13:38444000-38445400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:38444200-38445400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:38444200-38445400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr13:38444400-38445200	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr13:38444400-38445800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:38444600-38445200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
16	chr13:38444600-38445200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:38444600-38445200	Active TSS	Rectal Smooth Muscle	rectum
18	chr13:38444600-38445200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
19	chr13:38444600-38445400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:38444600-38445400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr13:38444600-38445400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:38444600-38445400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr13:38444600-38445400	Bivalent Enhancer	Fetal Heart	heart
24	chr13:38444600-38445400	Flanking Active TSS	NHDF-Ad	bronchial
25	chr13:38444600-38445400	Flanking Active TSS	NHLF	lung
26	chr13:38444600-38445400	Flanking Active TSS	Osteobl	bone
27	chr13:38444600-38445600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr13:38444600-38445600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:38444600-38445600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:38444600-38445600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:38444600-38445600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:38444600-38445600	Flanking Active TSS	NH-A	brain
33	chr13:38444600-38445600	Flanking Active TSS	NHEK	skin
34	chr13:38444800-38445200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:38444800-38445200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:38444800-38445200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
37	chr13:38444800-38445200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr13:38444800-38445200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
39	chr13:38444800-38445200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:38444800-38445200	Active TSS	Brain Germinal Matrix	brain
41	chr13:38444800-38445200	Active TSS	Brain Hippocampus Middle	brain
42	chr13:38444800-38445200	Enhancers	Colon Smooth Muscle	Colon
43	chr13:38444800-38445200	Bivalent Enhancer	HUVEC	blood vessel
44	chr13:38444800-38445400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:38444800-38445400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr13:38444800-38445400	Active TSS	Brain Anterior Caudate	brain
47	chr13:38444800-38445400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr13:38444800-38445400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
49	chr13:38444800-38445400	Bivalent Enhancer	HSMMtube	muscle
50	chr13:38444800-38445600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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