Variant report

Variant	rs12581489
Chromosome Location	chr12:25204106-25204107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:25203809-25206210	Raji	blood:	n/a	n/a
2	POLR2A	chr12:25204096-25206125	GM12878	blood:	n/a	n/a
3	MXI1	chr12:25203981-25206078	GM12878	blood:	n/a	n/a
4	RUNX3	chr12:25204063-25206227	GM12878	blood:	n/a	chr12:25205125-25205134 chr12:25205125-25205134
5	POLR2A	chr12:25204088-25206231	GM12891	blood:	n/a	n/a
6	MAZ	chr12:25204102-25206083	GM12878	blood:	n/a	chr12:25205483-25205492 chr12:25204668-25204677 chr12:25204670-25204677
7	POLR2A	chr12:25204105-25206480	GM12878	blood:	n/a	n/a
8	MTA3	chr12:25204014-25206071	GM12878	blood:	n/a	n/a
9	MTA3	chr12:25203955-25206246	GM12878	blood:	n/a	n/a
10	CHD1	chr12:25204001-25206646	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11608514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11609404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11610164	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11613116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12578652	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12578796	0.94[ASN][1000 genomes]
rs12579946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580818	1.00[AFR][1000 genomes]
rs16928338	1.00[AFR][1000 genomes]
rs16928340	1.00[AFR][1000 genomes]
rs16928352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16928354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72480019	1.00[AFR][1000 genomes]
rs73075629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73076090	1.00[AFR][1000 genomes]
rs73078105	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73078109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73078116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[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	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	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking 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	16 gene(s)	inside rSNPs	diseases
10	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers 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	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers 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 target site	16 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25200400-25205000	Weak transcription	Liver	Liver
2	chr12:25202800-25205600	Weak transcription	Stomach Mucosa	stomach
3	chr12:25203000-25204200	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:25203400-25204200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:25203600-25204200	Enhancers	Primary T cells from cord blood	blood
6	chr12:25203600-25204200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:25203600-25204200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:25203600-25204200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:25203600-25204200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:25203600-25204400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:25203800-25204200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr12:25203800-25204200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:25203800-25204200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:25203800-25204200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:25203800-25204200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:25203800-25204200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:25203800-25204800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr12:25203800-25204800	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:25203800-25205000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:25203800-25205000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:25203800-25205000	Flanking Active TSS	Dnd41	blood
22	chr12:25203800-25205200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr12:25204000-25204200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:25204000-25204200	Enhancers	Duodenum Mucosa	Duodenum
25	chr12:25204000-25204400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:25204000-25204400	Flanking Active TSS	Thymus	Thymus
27	chr12:25204000-25204600	Flanking Active TSS	Fetal Thymus	thymus
28	chr12:25204000-25204800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr12:25204000-25205000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr12:25204000-25208400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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