Variant report

Variant	rs12428965
Chromosome Location	chr13:111276123-111276124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111211377..111214970-chr13:111273880..111276435,4	MCF-7	breast:
2	chr13:111265898..111273230-chr13:111273500..111281065,16	MCF-7	breast:
3	chr13:111266306..111273367-chr13:111274094..111280494,12	K562	blood:
4	chr13:111266604..111270536-chr13:111275017..111281975,10	MCF-7	breast:
5	chr13:111271154..111277326-chr13:111363993..111367812,9	K562	blood:

Variant related genes	Relation type
ENSG00000139832	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1041143	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041173	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11069855	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11069856	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620520	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12429905	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12430333	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583083	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011692	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148081	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274411	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384426	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742193	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742194	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742196	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783097	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825465	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825466	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825467	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771700	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771701	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4773230	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61103246	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661645	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661647	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661650	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661656	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661657	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322067	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323602	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981194	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981780	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7995119	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9583518	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9588207	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9588209	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9588214	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
14	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription 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 target site	240 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12428965	AL139385.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:111269000-111277600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
5	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr13:111269600-111277200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:111269600-111279800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr13:111270400-111279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:111270400-111280200	Weak transcription	Fetal Heart	heart
10	chr13:111270400-111282800	Weak transcription	Fetal Kidney	kidney
11	chr13:111270800-111278000	Weak transcription	Small Intestine	intestine
12	chr13:111270800-111279800	Weak transcription	NH-A	brain
13	chr13:111270800-111296800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr13:111271200-111287000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:111271400-111277000	Weak transcription	Stomach Mucosa	stomach
16	chr13:111271400-111281400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:111271600-111281600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:111273400-111277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr13:111273400-111281200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:111274000-111278200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:111274200-111278000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:111274400-111276200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr13:111274400-111277800	Strong transcription	Hela-S3	cervix
24	chr13:111274400-111278400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr13:111274400-111284400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr13:111274600-111276200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:111274600-111276200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr13:111274600-111276200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr13:111274600-111276200	Strong transcription	Aorta	Aorta
30	chr13:111274600-111276200	Strong transcription	Brain Germinal Matrix	brain
31	chr13:111274600-111276200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr13:111274600-111276200	Strong transcription	Colonic Mucosa	Colon
33	chr13:111274600-111276200	Strong transcription	Fetal Lung	lung
34	chr13:111274600-111276400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:111274600-111276600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr13:111274600-111277200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:111274600-111277200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr13:111274600-111277200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:111274600-111277200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr13:111274600-111277200	Strong transcription	HepG2	liver
41	chr13:111274600-111277400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:111274600-111277400	Strong transcription	Fetal Muscle Leg	muscle
43	chr13:111274600-111277600	Strong transcription	Fetal Intestine Large	intestine
44	chr13:111274600-111277600	Strong transcription	Fetal Stomach	stomach
45	chr13:111274600-111277800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:111274600-111277800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:111274600-111277800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr13:111274600-111278000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:111274600-111278000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:111274600-111278000	Strong transcription	GM12878-XiMat	blood

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