Variant report

Variant	rs12659038
Chromosome Location	chr5:96208824-96208825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96207193..96215079-chr5:96269183..96273335,11	MCF-7	breast:
2	chr5:96207921..96209520-chr5:96223950..96226195,2	K562	blood:
3	chr5:96207915..96210416-chr5:96223446..96226195,4	K562	blood:

Variant related genes	Relation type
ENSG00000164308	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1230366	0.84[ASN][1000 genomes]
rs12519842	0.84[ASN][1000 genomes]
rs12659825	0.84[ASN][1000 genomes]
rs151823	0.82[ASN][1000 genomes]
rs152468	0.84[ASN][1000 genomes]
rs17087066	0.83[AMR][1000 genomes]
rs184971	0.84[ASN][1000 genomes]
rs2042381	0.82[ASN][1000 genomes]
rs2351012	0.84[ASN][1000 genomes]
rs2351013	0.84[ASN][1000 genomes]
rs245472	0.84[ASN][1000 genomes]
rs249960	0.83[ASN][1000 genomes]
rs2545629	0.84[ASN][1000 genomes]
rs2549804	0.84[ASN][1000 genomes]
rs2549805	0.84[ASN][1000 genomes]
rs26493	0.82[ASN][1000 genomes]
rs27694	0.84[ASN][1000 genomes]
rs2911138	0.82[ASN][1000 genomes]
rs2911139	0.82[ASN][1000 genomes]
rs2927619	0.84[ASN][1000 genomes]
rs2927620	0.84[ASN][1000 genomes]
rs34735	0.84[ASN][1000 genomes]
rs3985002	0.84[ASN][1000 genomes]
rs61112531	0.84[ASN][1000 genomes]
rs61484219	0.85[AMR][1000 genomes]
rs709668	0.84[ASN][1000 genomes]
rs845028	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96196600-96211400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:96201200-96210200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:96202000-96211400	Weak transcription	Liver	Liver
4	chr5:96202600-96209600	Weak transcription	Fetal Intestine Large	intestine
5	chr5:96203000-96211400	Weak transcription	Stomach Mucosa	stomach
6	chr5:96204800-96211600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr5:96205000-96209600	Weak transcription	Fetal Intestine Small	intestine
8	chr5:96205000-96211400	Weak transcription	Brain Angular Gyrus	brain
9	chr5:96205600-96211400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:96206200-96211400	Weak transcription	Adipose Nuclei	Adipose
11	chr5:96206400-96209000	Weak transcription	K562	blood
12	chr5:96206400-96209600	Enhancers	Dnd41	blood
13	chr5:96206400-96210200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:96206400-96211400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:96206400-96211400	Weak transcription	NHEK	skin
16	chr5:96206400-96211400	Weak transcription	Osteobl	bone
17	chr5:96206600-96211400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:96206600-96211400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:96206600-96211400	Weak transcription	HMEC	breast
20	chr5:96206600-96211600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:96206800-96211000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:96206800-96211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:96206800-96211400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:96207000-96209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:96207000-96209400	Weak transcription	Brain Anterior Caudate	brain
26	chr5:96207000-96210000	Weak transcription	HepG2	liver
27	chr5:96207000-96210800	Weak transcription	Fetal Thymus	thymus
28	chr5:96207000-96211000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:96207000-96211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:96207000-96211400	Weak transcription	Brain Substantia Nigra	brain
31	chr5:96207000-96211600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:96207200-96210600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:96207200-96211200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:96207200-96211400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:96207200-96211400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:96207200-96211400	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:96207200-96211600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:96207200-96211600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:96207400-96211800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:96207600-96210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:96207600-96211600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:96207600-96212000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:96207800-96209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:96208000-96210600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:96208000-96211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:96208200-96209600	Enhancers	GM12878-XiMat	blood
47	chr5:96208200-96210000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr5:96208200-96210000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:96208200-96210600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:96208200-96211400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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