Variant report

Variant	rs12310887
Chromosome Location	chr12:25246368-25246369
allele	C/T
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	chr12:25245542-25247815	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:25246022-25246665	GM12878	blood:	n/a	n/a
3	SPI1	chr12:25246275-25246600	GM12891	blood:	n/a	chr12:25246492-25246501

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CASC1-2	chr12:25245649-25246834	NONHSAT027340

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11047859	0.89[AMR][1000 genomes]
rs11047869	0.89[AMR][1000 genomes]
rs11829456	0.89[AMR][1000 genomes]
rs12307064	0.89[AMR][1000 genomes]
rs12309185	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4495968	1.00[CEU][hapmap]
rs7133635	1.00[CEU][hapmap]
rs7134445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304274	0.89[AMR][1000 genomes]
rs73079682	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7316187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953861	0.89[AMR][1000 genomes]
rs7972282	0.89[AMR][1000 genomes]
rs7978771	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	esv2757492	chr12:25233781-25252178	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2759884	chr12:25233781-25252178	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25212000-25250800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:25227400-25251000	Weak transcription	Pancreas	Pancrea
7	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
9	chr12:25232000-25247600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:25234000-25246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:25234800-25247000	Strong transcription	Primary T cells from cord blood	blood
13	chr12:25238600-25251000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
15	chr12:25238600-25265200	Weak transcription	Lung	lung
16	chr12:25238800-25251000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:25239800-25253200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:25240000-25251000	Weak transcription	Spleen	Spleen
19	chr12:25241000-25248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:25242600-25247800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:25243000-25247200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:25243000-25249000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:25243200-25250800	Weak transcription	Liver	Liver
26	chr12:25243400-25246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:25243600-25249400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:25244400-25249000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:25245000-25247000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:25246000-25246400	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:25246000-25246400	Genic enhancers	Primary B cells from cord blood	blood
32	chr12:25246000-25246400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr12:25246000-25247200	ZNF genes & repeats	GM12878-XiMat	blood
34	chr12:25246000-25247600	ZNF genes & repeats	Dnd41	blood
35	chr12:25246200-25246400	Enhancers	Ovary	ovary
36	chr12:25246200-25247000	ZNF genes & repeats	Thymus	Thymus
37	chr12:25246200-25247400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr12:25246200-25247600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr12:25246200-25247600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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