Variant report

Variant	rs2306701
Chromosome Location	chr12:25241360-25241361
allele	A/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	chr12:25239096-25241548	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:25240395-25241713	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:25240260-25241443	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25232452..25234531-chr12:25239537..25241668,2	MCF-7	breast:

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10842462	0.94[ASN][1000 genomes]
rs11047821	0.92[ASN][1000 genomes]
rs12426684	1.00[JPT][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2306701	CMAS	cis	parietal	SCAN
rs2306701	LOC144363	cis	multi-tissue	Pritchard
rs2306701	CASC1	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr12:25214400-25245600	Weak transcription	Ovary	ovary
5	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:25224600-25241600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:25227400-25251000	Weak transcription	Pancreas	Pancrea
9	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:25229200-25241400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
12	chr12:25231800-25246000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:25232000-25241400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:25232000-25241600	Strong transcription	Dnd41	blood
15	chr12:25232000-25247600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:25233200-25242200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:25233800-25242200	Strong transcription	Primary B cells from cord blood	blood
19	chr12:25234000-25246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:25234800-25247000	Strong transcription	Primary T cells from cord blood	blood
21	chr12:25235000-25242000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:25236400-25241400	Weak transcription	Liver	Liver
23	chr12:25238600-25251000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
25	chr12:25238600-25265200	Weak transcription	Lung	lung
26	chr12:25238800-25251000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:25239800-25253200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:25240000-25242400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:25240000-25242600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:25240000-25251000	Weak transcription	Spleen	Spleen
31	chr12:25240400-25241400	Genic enhancers	Thymus	Thymus
32	chr12:25240400-25241600	Enhancers	HUVEC	blood vessel
33	chr12:25240600-25241400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:25240600-25243200	Genic enhancers	Primary hematopoietic stem cells	blood
35	chr12:25240600-25243200	Genic enhancers	GM12878-XiMat	blood
36	chr12:25240600-25243400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:25240800-25241400	Enhancers	Adipose Nuclei	Adipose
38	chr12:25241000-25242800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:25241000-25248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:25241200-25241400	Enhancers	Stomach Mucosa	stomach
41	chr12:25241200-25242000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:25241200-25243000	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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