Variant report

Variant	rs721438
Chromosome Location	chr12:106890059-106890060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106882122..106884058-chr12:106888578..106890580,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1004601	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778482	0.90[ASN][1000 genomes]
rs12424092	0.84[ASN][1000 genomes]
rs1882413	0.85[CHB][hapmap]
rs2243506	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs2244958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2245062	0.86[CHB][hapmap]
rs2250262	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2254755	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2264759	0.83[ASN][1000 genomes]
rs2288270	0.96[ASN][1000 genomes]
rs7137444	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137638	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303737	0.88[AMR][1000 genomes]
rs7313412	0.92[ASN][1000 genomes]
rs7315611	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs721438	TCP11L2	cis	cerebellum	SCAN
rs721438	ANO1	trans	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
4	chr12:106855800-106895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:106855800-106896200	Weak transcription	Thymus	Thymus
6	chr12:106856000-106893000	Weak transcription	Right Ventricle	heart
7	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:106857200-106890200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:106858600-106895400	Weak transcription	Fetal Heart	heart
10	chr12:106865200-106890600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:106865200-106892400	Weak transcription	Aorta	Aorta
12	chr12:106865400-106890400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:106865400-106890400	Weak transcription	Colonic Mucosa	Colon
14	chr12:106865400-106890400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:106865400-106891800	Weak transcription	Gastric	stomach
16	chr12:106865400-106893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:106865400-106895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:106865400-106897800	Weak transcription	Spleen	Spleen
19	chr12:106865600-106890200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:106865600-106890200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:106865600-106890400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:106865600-106890400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:106865600-106890400	Weak transcription	Dnd41	blood
26	chr12:106865600-106891000	Weak transcription	Brain Angular Gyrus	brain
27	chr12:106865600-106891200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:106865600-106891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:106865600-106891400	Weak transcription	Fetal Lung	lung
30	chr12:106865600-106891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:106865600-106894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:106872200-106891800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:106872600-106897800	Weak transcription	Psoas Muscle	Psoas
34	chr12:106873600-106890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:106873800-106890800	Weak transcription	Hela-S3	cervix
36	chr12:106874200-106890400	Weak transcription	HSMMtube	muscle
37	chr12:106879800-106890600	Enhancers	Brain Germinal Matrix	brain
38	chr12:106881800-106893000	Weak transcription	K562	blood
39	chr12:106883800-106891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:106884000-106893200	Weak transcription	NH-A	brain
41	chr12:106884400-106891800	Weak transcription	NHEK	skin
42	chr12:106884800-106891400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:106884800-106899800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:106886000-106891800	Weak transcription	HUVEC	blood vessel
45	chr12:106886200-106916400	Weak transcription	A549	lung
46	chr12:106886600-106890800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:106887200-106893400	Weak transcription	Fetal Intestine Large	intestine
48	chr12:106887600-106895400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:106887600-106898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine

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