Variant report

Variant	rs1644242
Chromosome Location	chr5:112057679-112057680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112056712..112059185-chr5:112067106..112069826,2	K562	blood:
2	chr5:112053504..112055952-chr5:112056185..112057959,2	MCF-7	breast:
3	chr5:112040021..112044841-chr5:112056606..112060085,6	K562	blood:
4	chr5:112038553..112041521-chr5:112056606..112058817,2	K562	blood:
5	chr5:112056525..112058948-chr5:112060901..112062604,2	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11953943	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11960216	0.93[EUR][1000 genomes]
rs1644241	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1661032	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1661034	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1697914	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1697916	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17134960	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1734244	0.91[EUR][1000 genomes]
rs1734245	0.90[CEU][hapmap]
rs1734246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1734247	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1882619	0.95[GIH][hapmap]
rs2431505	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2431507	0.90[CEU][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes]
rs2431508	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2431509	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2431511	0.95[EUR][1000 genomes]
rs2439590	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2439592	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2439593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2439594	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2455294	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2455296	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2464802	0.83[EUR][1000 genomes]
rs2464808	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2464810	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909784	0.95[EUR][1000 genomes]
rs2909961	0.95[EUR][1000 genomes]
rs2909962	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs73220022	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112044800-112058000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:112044800-112058800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:112045400-112062000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:112045600-112060200	Weak transcription	NHLF	lung
5	chr5:112045600-112061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:112045600-112063600	Weak transcription	Ovary	ovary
7	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:112047000-112060400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:112047000-112061600	Weak transcription	Aorta	Aorta
10	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:112047400-112058600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:112047400-112060400	Weak transcription	Fetal Intestine Large	intestine
13	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
14	chr5:112047600-112061600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:112048200-112058200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:112048400-112061200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:112049200-112061600	Weak transcription	Fetal Stomach	stomach
18	chr5:112049600-112060400	Weak transcription	Lung	lung
19	chr5:112051200-112058600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
21	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:112054400-112058200	Weak transcription	Psoas Muscle	Psoas
23	chr5:112054400-112058400	Weak transcription	Left Ventricle	heart
24	chr5:112054400-112060600	Weak transcription	Small Intestine	intestine
25	chr5:112054400-112062200	Weak transcription	Right Ventricle	heart
26	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
27	chr5:112054600-112061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:112054800-112058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:112054800-112058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:112054800-112060200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:112055000-112061600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:112056200-112059600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:112056400-112058000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:112056400-112058600	Weak transcription	Brain Anterior Caudate	brain
35	chr5:112056400-112060800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:112056400-112061800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:112056600-112058000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:112056600-112066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:112056600-112067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:112056800-112061800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:112056800-112063800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:112057200-112057800	Enhancers	Brain Substantia Nigra	brain
43	chr5:112057200-112059000	Enhancers	Brain Hippocampus Middle	brain
44	chr5:112057400-112058400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:112057400-112058400	Weak transcription	Fetal Brain Female	brain
46	chr5:112057400-112058400	Weak transcription	Right Atrium	heart
47	chr5:112057400-112059200	Enhancers	Colon Smooth Muscle	Colon
48	chr5:112057400-112060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:112057400-112064800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:112057600-112057800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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