Variant report

Variant	rs1497259
Chromosome Location	chr12:25207653-25207654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10842453	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10842454	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs952265	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
5	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh 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
8	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
12	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv52528	chr12:25204785-25213609	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1497259	LYRM5	cis	parietal	SCAN
rs1497259	REP15	cis	cerebellum	SCAN
rs1497259	BCAT1	cis	lymphoblastoid	seeQTL
rs1497259	BCAT1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25204000-25208400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:25204200-25208000	Active TSS	Rectal Smooth Muscle	rectum
3	chr12:25204400-25208200	Active TSS	Adipose Nuclei	Adipose
4	chr12:25204400-25209200	Active TSS	Duodenum Mucosa	Duodenum
5	chr12:25204400-25210200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr12:25204800-25208000	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:25204800-25209000	Active TSS	Primary T cells fromperipheralblood	blood
8	chr12:25204800-25209000	Active TSS	Thymus	Thymus
9	chr12:25204800-25209000	Active TSS	GM12878-XiMat	blood
10	chr12:25204800-25209600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:25205000-25207800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:25205000-25207800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:25205000-25207800	Active TSS	Right Atrium	heart
14	chr12:25205000-25209000	Active TSS	Primary B cells from peripheral blood	blood
15	chr12:25205000-25209000	Active TSS	Fetal Thymus	thymus
16	chr12:25205000-25220000	Weak transcription	Spleen	Spleen
17	chr12:25205400-25207800	Active TSS	Primary monocytes fromperipheralblood	blood
18	chr12:25205400-25207800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:25205600-25207800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:25205800-25224800	Weak transcription	Lung	lung
21	chr12:25206000-25217600	Weak transcription	Pancreas	Pancrea
22	chr12:25206200-25208800	Weak transcription	Stomach Mucosa	stomach
23	chr12:25206200-25209000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:25206400-25210200	Enhancers	HMEC	breast
25	chr12:25206600-25208000	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr12:25206800-25207800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:25206800-25208200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr12:25206800-25208400	Flanking Active TSS	Dnd41	blood
29	chr12:25206800-25209800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr12:25206800-25210000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:25207000-25208000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:25207000-25208000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:25207000-25208200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:25207000-25208200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr12:25207000-25208200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:25207000-25210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:25207200-25207800	Active TSS	Brain Angular Gyrus	brain
38	chr12:25207200-25207800	Active TSS	Brain Anterior Caudate	brain
39	chr12:25207200-25208000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:25207200-25208000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr12:25207200-25208000	Enhancers	NH-A	brain
42	chr12:25207200-25208000	Flanking Active TSS	NHEK	skin
43	chr12:25207200-25208200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr12:25207200-25208400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:25207200-25210200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:25207400-25207800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:25207400-25207800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:25207400-25207800	Active TSS	Ovary	ovary
49	chr12:25207400-25207800	Active TSS	K562	blood
50	chr12:25207400-25208200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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