Variant report

Variant	rs4662369
Chromosome Location	chr2:144938116-144938117
allele	A/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	JUN	chr2:144937932-144938132	K562	blood:	n/a	n/a
2	POLR2A	chr2:144938110-144938392	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:144934903..144937420-chr2:144937432..144939310,2	K562	blood:

Variant related genes	Relation type
GTDC1	TF binding region
ENSG00000121964	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10173322	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197599	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10439175	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10439191	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615549	0.87[TSI][hapmap]
rs13406608	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13406634	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411437	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13415860	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13416245	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344628	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1429096	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1429098	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1465366	0.87[TSI][hapmap]
rs16823379	0.90[EUR][1000 genomes]
rs16823411	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16823476	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16823541	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16848271	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16855315	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2303544	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420848	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28479091	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705915	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806478	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs3806479	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3806480	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4662361	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4662362	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4662363	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4662368	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55681388	0.91[EUR][1000 genomes]
rs55766236	1.00[EUR][1000 genomes]
rs55803436	1.00[EUR][1000 genomes]
rs55922892	1.00[EUR][1000 genomes]
rs56048525	1.00[EUR][1000 genomes]
rs56181240	1.00[EUR][1000 genomes]
rs56203039	1.00[EUR][1000 genomes]
rs56271766	1.00[EUR][1000 genomes]
rs56302598	0.84[EUR][1000 genomes]
rs56317913	1.00[EUR][1000 genomes]
rs56361359	1.00[EUR][1000 genomes]
rs6707579	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726343	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73008247	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73964929	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7563626	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs959766	0.87[TSI][hapmap]
rs959767	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1005376	chr2:144803630-144968946	Enhancers Weak transcription 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	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
9	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
10	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
11	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
12	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
13	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144923600-144941200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:144923800-144955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:144924400-144939200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:144928000-144941400	Weak transcription	Lung	lung
5	chr2:144928000-144943400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:144928200-144965400	Weak transcription	Left Ventricle	heart
7	chr2:144929600-144941200	Weak transcription	Fetal Brain Female	brain
8	chr2:144931200-144941400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:144931200-144951800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:144931400-144973800	Weak transcription	Ovary	ovary
11	chr2:144931600-144941400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:144931600-144944600	Weak transcription	Liver	Liver
13	chr2:144932000-144941200	Weak transcription	Adipose Nuclei	Adipose
14	chr2:144932000-144960600	Weak transcription	HSMMtube	muscle
15	chr2:144932000-144965000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:144932200-144938200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:144932200-144955400	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:144934800-144940800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:144935600-144939800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:144936400-144938200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:144936400-144940800	Weak transcription	Primary T cells from cord blood	blood
22	chr2:144936400-144941400	Weak transcription	Fetal Lung	lung
23	chr2:144936600-144941000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:144936800-144941000	Weak transcription	Primary B cells from cord blood	blood
25	chr2:144936800-144941200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:144937400-144938600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:144937600-144955400	Weak transcription	Fetal Intestine Small	intestine
28	chr2:144937800-144938400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:144938000-144938600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:144938000-144939200	Enhancers	NHDF-Ad	bronchial

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