Variant report

Variant	rs1497260
Chromosome Location	chr12:25208996-25208997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10505958	1.00[AFR][1000 genomes]
rs11047791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047793	0.89[ASN][1000 genomes]
rs11047794	0.89[ASN][1000 genomes]
rs11047796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047797	1.00[ASN][1000 genomes]
rs11047803	1.00[AFR][1000 genomes]
rs12226955	1.00[ASN][1000 genomes]
rs12228264	1.00[ASN][1000 genomes]
rs12427285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319335	1.00[ASN][1000 genomes]
rs1497250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012450	1.00[ASN][1000 genomes]
rs859123	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25204400-25209200	Active TSS	Duodenum Mucosa	Duodenum
2	chr12:25204400-25210200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:25204800-25209000	Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:25204800-25209000	Active TSS	Thymus	Thymus
5	chr12:25204800-25209000	Active TSS	GM12878-XiMat	blood
6	chr12:25204800-25209600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:25205000-25209000	Active TSS	Primary B cells from peripheral blood	blood
8	chr12:25205000-25209000	Active TSS	Fetal Thymus	thymus
9	chr12:25205000-25220000	Weak transcription	Spleen	Spleen
10	chr12:25205800-25224800	Weak transcription	Lung	lung
11	chr12:25206000-25217600	Weak transcription	Pancreas	Pancrea
12	chr12:25206200-25209000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:25206400-25210200	Enhancers	HMEC	breast
14	chr12:25206800-25209800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr12:25206800-25210000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:25207000-25210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:25207200-25210200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:25207400-25210000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr12:25207400-25219400	Weak transcription	Liver	Liver
20	chr12:25207600-25209000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr12:25207600-25209000	Weak transcription	Small Intestine	intestine
22	chr12:25207600-25210000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:25207600-25214200	Weak transcription	Fetal Intestine Large	intestine
24	chr12:25207800-25209000	Weak transcription	Right Atrium	heart
25	chr12:25207800-25221400	Weak transcription	Brain Angular Gyrus	brain
26	chr12:25208000-25209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:25208000-25209200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:25208000-25209800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr12:25208000-25210200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr12:25208000-25210200	Enhancers	NHEK	skin
31	chr12:25208000-25211000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:25208200-25209000	Weak transcription	Adipose Nuclei	Adipose
33	chr12:25208200-25210200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:25208200-25210800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:25208200-25211200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:25208200-25212200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:25208200-25216600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:25208400-25209000	Enhancers	Dnd41	blood
39	chr12:25208400-25209800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:25208600-25209200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr12:25208600-25210200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr12:25208600-25211200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr12:25208800-25209200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr12:25208800-25209200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr12:25208800-25210000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:25208800-25210000	Enhancers	Stomach Mucosa	stomach
47	chr12:25208800-25210200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr12:25208800-25210200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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