Variant report

Variant	rs1731597
Chromosome Location	chr3:116164641-116164642
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	CTBP2	chr3:116163661-116164948	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr3:116163676-116165076	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:116163859-116164723	SK-N-MC	brain:	n/a	n/a
4	FOXP2	chr3:116164149-116164665	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr3:116164631-116164645	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:116163545-116164650	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:116162922-116164945	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr3:116164477-116164646	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr3:116163671-116165020	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LSAMP	TF binding region

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1713001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1713007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1731598	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1731601	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1731610	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795249	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1795263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920193	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864815	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2902853	0.92[CEU][hapmap]
rs3866148	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4626095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4831140	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116160400-116165000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:116160600-116165200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:116161000-116164800	Active TSS	Fetal Brain Female	brain
4	chr3:116161000-116165200	Active TSS	Brain Substantia Nigra	brain
5	chr3:116161600-116164800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:116163000-116164800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:116163000-116164800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:116163400-116164800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:116163400-116164800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:116163400-116164800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:116163600-116164800	Active TSS	Stomach Smooth Muscle	stomach
12	chr3:116163600-116165200	Active TSS	Brain Anterior Caudate	brain
13	chr3:116163800-116164800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:116164000-116164800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:116164200-116169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:116164400-116164800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:116164400-116165000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:116164400-116165000	Enhancers	Fetal Muscle Leg	muscle
19	chr3:116164400-116165200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:116164400-116165200	Enhancers	Fetal Lung	lung
21	chr3:116164400-116165400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:116164600-116164800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr3:116164600-116164800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:116164600-116164800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:116164600-116164800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:116164600-116164800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:116164600-116164800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:116164600-116164800	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr3:116164600-116164800	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr3:116164600-116164800	Flanking Active TSS	Fetal Stomach	stomach
31	chr3:116164600-116164800	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr3:116164600-116165000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:116164600-116165000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:116164600-116165000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr3:116164600-116165000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr3:116164600-116165000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:116164600-116165000	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr3:116164600-116165000	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr3:116164600-116165000	Flanking Active TSS	Fetal Brain Male	brain
40	chr3:116164600-116165200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:116164600-116165200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:116164600-116165200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:116164600-116165400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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