Variant report

Variant	rs16823583
Chromosome Location	chr2:144969618-144969619
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	NFYB	chr2:144969467-144969733	GM12878	blood:	n/a	n/a
2	REST	chr2:144969392-144969685	PFSK-1	brain:	n/a	chr2:144969568-144969577
3	EP300	chr2:144969288-144969729	K562	blood:	n/a	chr2:144969323-144969337 chr2:144969317-144969331 chr2:144969319-144969333 chr2:144969322-144969336
4	JUN	chr2:144969360-144969787	K562	blood:	n/a	n/a
5	REST	chr2:144969445-144969689	K562	blood:	n/a	chr2:144969568-144969577
6	POLR2A	chr2:144969462-144970238	K562	blood:	n/a	n/a
7	NFYB	chr2:144969442-144969792	K562	blood:	n/a	n/a
8	REST	chr2:144969418-144969662	PFSK-1	brain:	n/a	chr2:144969568-144969577

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1012272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151646	0.85[EUR][1000 genomes]
rs12328646	0.82[LWK][hapmap]
rs12620547	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12622422	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432930	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823569	0.85[CHB][hapmap];0.95[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60152197	0.85[EUR][1000 genomes]
rs62167058	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62167059	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169169	0.83[EUR][1000 genomes]
rs62169170	0.81[EUR][1000 genomes]
rs6708537	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758720	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1013338	chr2:144806920-144969818	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv834396	chr2:144842187-145019465	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144931400-144973800	Weak transcription	Ovary	ovary
2	chr2:144948800-144973600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:144952200-144973400	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:144952800-144971200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:144953600-144971400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr2:144955800-144969800	Weak transcription	Placenta	Placenta
7	chr2:144955800-144969800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:144955800-144973400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:144955800-144981200	Weak transcription	Fetal Intestine Large	intestine
10	chr2:144956200-144971400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:144956200-144973400	Weak transcription	Small Intestine	intestine
12	chr2:144956200-144973400	Weak transcription	K562	blood
13	chr2:144956200-144976000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:144956200-144985200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:144959000-144973600	Weak transcription	Brain Substantia Nigra	brain
16	chr2:144959800-144975800	Weak transcription	NHLF	lung
17	chr2:144959800-144977600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:144960000-144975600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:144960000-144975800	Weak transcription	NHDF-Ad	bronchial
20	chr2:144960800-144970800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:144961000-144973400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:144962600-144998600	Weak transcription	Psoas Muscle	Psoas
23	chr2:144962800-144975600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:144963000-144973600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:144963000-144978000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:144963400-144970600	Weak transcription	GM12878-XiMat	blood
27	chr2:144963400-144973400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:144963800-144970600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:144963800-144971400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:144964400-144971200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:144964400-144973800	Weak transcription	Aorta	Aorta
32	chr2:144964400-144998200	Weak transcription	Fetal Kidney	kidney
33	chr2:144965400-145010000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:144965600-144973800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:144965600-144992400	Weak transcription	Fetal Stomach	stomach
36	chr2:144965800-144977200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:144966000-144970200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:144966000-144973600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:144966000-144973800	Weak transcription	Primary T cells from cord blood	blood
40	chr2:144966200-144973400	Weak transcription	Adipose Nuclei	Adipose
41	chr2:144966200-144973400	Weak transcription	Brain Angular Gyrus	brain
42	chr2:144966200-144973600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:144966200-144973600	Weak transcription	Primary B cells from cord blood	blood
44	chr2:144966200-144976000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:144966400-144978000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:144966800-144977000	Weak transcription	Left Ventricle	heart
47	chr2:144967200-144971400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:144967800-144970000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:144968600-144973600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:144968600-144973800	Weak transcription	Primary hematopoietic stem cells	blood

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