Variant report

Variant	rs42872
Chromosome Location	chr5:53390040-53390041
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs156381	0.86[JPT][hapmap]
rs156382	0.85[JPT][hapmap]
rs156436	0.81[JPT][hapmap]
rs156441	0.82[JPT][hapmap]
rs156443	0.86[JPT][hapmap]
rs156829	0.82[JPT][hapmap]
rs2547538	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs255766	0.82[JPT][hapmap]
rs273219	0.82[JPT][hapmap]
rs273220	0.82[JPT][hapmap]
rs274373	0.82[JPT][hapmap]
rs279744	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs35006	0.90[CEU][hapmap]
rs682103	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs696195	0.85[YRI][hapmap]
rs7719836	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
7	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
16	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
17	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
21	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
22	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
23	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53357000-53408000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr5:53365200-53391200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:53377400-53412200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:53377600-53390800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:53377800-53408600	Weak transcription	Primary B cells from cord blood	blood
6	chr5:53380200-53394200	Weak transcription	Spleen	Spleen
7	chr5:53380600-53408600	Weak transcription	Fetal Intestine Large	intestine
8	chr5:53380800-53399400	Weak transcription	Primary T cells from cord blood	blood
9	chr5:53380800-53408600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:53384400-53391000	Weak transcription	Fetal Kidney	kidney
11	chr5:53386200-53390600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:53386200-53391600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:53386800-53391200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:53386800-53391200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:53386800-53393600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:53387000-53390200	Enhancers	Rectal Smooth Muscle	rectum
17	chr5:53387000-53391000	Enhancers	Colon Smooth Muscle	Colon
18	chr5:53387400-53393600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:53387400-53400200	Weak transcription	Pancreas	Pancrea
20	chr5:53387600-53399800	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:53387800-53390800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:53387800-53394000	Weak transcription	Aorta	Aorta
23	chr5:53387800-53395400	Weak transcription	Psoas Muscle	Psoas
24	chr5:53387800-53399400	Weak transcription	K562	blood
25	chr5:53387800-53402800	Weak transcription	Lung	lung
26	chr5:53388400-53391600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:53388600-53391200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:53389000-53390400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:53389000-53391600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr5:53389200-53390600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:53389200-53390600	Weak transcription	Brain Substantia Nigra	brain
32	chr5:53389400-53390400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:53389400-53390400	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:53389400-53391000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:53389400-53391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:53389400-53391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:53389400-53391600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:53389400-53393600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:53389400-53394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:53389400-53416400	Weak transcription	Left Ventricle	heart
41	chr5:53389800-53390800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:53389800-53393600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:53390000-53391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:53390000-53404200	Weak transcription	NHEK	skin
45	chr5:53390000-53405600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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