Variant report

Variant	rs11046275
Chromosome Location	chr12:22203908-22203909
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	chr12:22202871-22204854	K562	blood:	n/a	n/a
2	POLR2A	chr12:22203573-22204029	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:22197898..22202531-chr12:22202616..22208309,9	MCF-7	breast:
2	chr12:22201346..22204337-chr12:22211554..22214294,3	K562	blood:
3	chr12:22202159..22205097-chr12:22205355..22208249,2	K562	blood:

Variant related genes	Relation type
CMAS	TF binding region
ENSG00000111726	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10841929	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841931	0.91[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841932	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841933	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841934	0.91[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841935	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs10841936	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11046276	0.91[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046281	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11046289	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046290	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046291	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046292	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046297	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2058849	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2111352	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2216296	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2418037	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2418038	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2955503	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs2955515	0.91[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2970800	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809204	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487268	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487272	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487273	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487275	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487276	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135019	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731355	0.93[ASN][1000 genomes]
rs7316741	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7316854	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs759582	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758298	chr12:22140834-22339299	Enhancers Active TSS Strong transcription Weak transcription 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	11 gene(s)	inside rSNPs	diseases
3	esv2759883	chr12:22140834-22736907	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv438196	chr12:22195202-22234058	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1850259	chr12:22198865-22244741	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11046275	IFLTD1	cis	cerebellum	SCAN
rs11046275	CMAS	cis	cerebellum	SCAN
rs11046275	PYROXD1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22200000-22208400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:22200000-22209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:22200000-22209400	Weak transcription	Spleen	Spleen
4	chr12:22200000-22214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:22200000-22218200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:22200000-22220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:22200000-22220200	Weak transcription	Lung	lung
8	chr12:22200200-22208200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:22200200-22208400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:22200200-22208600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:22200200-22208800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:22200200-22209000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:22200200-22209000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:22200200-22209200	Weak transcription	Primary B cells from cord blood	blood
15	chr12:22200200-22209200	Weak transcription	Right Ventricle	heart
16	chr12:22200200-22209200	Weak transcription	HSMM	muscle
17	chr12:22200200-22209400	Weak transcription	Left Ventricle	heart
18	chr12:22200200-22209400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:22200200-22215200	Weak transcription	HSMMtube	muscle
20	chr12:22200200-22215800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:22200200-22219600	Weak transcription	Aorta	Aorta
22	chr12:22200400-22208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:22200400-22208600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:22200400-22209200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:22200400-22216600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:22200400-22220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:22200800-22205200	Enhancers	Fetal Intestine Small	intestine
28	chr12:22200800-22207000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:22200800-22208400	Weak transcription	Osteobl	bone
30	chr12:22200800-22208600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:22200800-22208800	Weak transcription	NH-A	brain
32	chr12:22200800-22209000	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:22200800-22209400	Weak transcription	Brain Germinal Matrix	brain
34	chr12:22200800-22209400	Weak transcription	Brain Substantia Nigra	brain
35	chr12:22200800-22209400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:22200800-22209400	Weak transcription	NHLF	lung
37	chr12:22200800-22210800	Weak transcription	Fetal Stomach	stomach
38	chr12:22200800-22220800	Weak transcription	Fetal Heart	heart
39	chr12:22201200-22207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:22201200-22208200	Weak transcription	NHDF-Ad	bronchial
41	chr12:22201200-22208600	Weak transcription	Fetal Kidney	kidney
42	chr12:22201200-22209000	Weak transcription	HUVEC	blood vessel
43	chr12:22201200-22209200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:22201200-22209200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:22201200-22209400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:22201200-22211400	Weak transcription	Hela-S3	cervix
47	chr12:22201400-22204400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:22201400-22209000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:22201400-22220400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:22201600-22204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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