Variant report

Variant	rs2955515
Chromosome Location	chr12:22221159-22221160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:22219317..22222096-chr12:22223518..22225466,2	K562	blood:
2	chr12:22220400..22223004-chr12:22489207..22490731,2	K562	blood:

Variant related genes	Relation type
ENSG00000111728	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10841928	0.80[AMR][1000 genomes]
rs10841929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841931	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841936	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11046275	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]
rs11046276	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046281	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11046289	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046290	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046291	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046292	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046297	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058849	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111352	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2216296	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418037	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2970800	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809204	0.90[ASN][1000 genomes]
rs61921546	0.82[ASN][1000 genomes]
rs6487268	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487272	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487273	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487276	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135019	0.80[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731355	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316741	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316854	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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
rs2955515	CMAS	cis	cerebellum	SCAN
rs2955515	IFLTD1	cis	cerebellum	SCAN
rs2955515	RASSF8	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22202200-22223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:22203800-22235200	Weak transcription	Gastric	stomach
3	chr12:22204600-22223400	Weak transcription	Pancreas	Pancrea
4	chr12:22205200-22222200	Weak transcription	Fetal Intestine Small	intestine
5	chr12:22209800-22222000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:22209800-22223200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:22209800-22229200	Weak transcription	Thymus	Thymus
8	chr12:22210000-22221200	Strong transcription	Liver	Liver
9	chr12:22210400-22221200	Weak transcription	Right Ventricle	heart
10	chr12:22213000-22221200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:22216000-22221200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:22216000-22221800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:22216200-22222200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:22216200-22233200	Weak transcription	K562	blood
15	chr12:22216400-22221200	Weak transcription	Fetal Brain Female	brain
16	chr12:22216600-22221200	Weak transcription	NHDF-Ad	bronchial
17	chr12:22217800-22221200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:22217800-22222000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr12:22218400-22221200	Weak transcription	Colonic Mucosa	Colon
20	chr12:22218800-22221400	Weak transcription	HUVEC	blood vessel
21	chr12:22218800-22222000	Weak transcription	HSMM	muscle
22	chr12:22218800-22222400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:22218800-22222600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:22218800-22223000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:22219000-22222400	Weak transcription	A549	lung
26	chr12:22219000-22222600	Weak transcription	HSMMtube	muscle
27	chr12:22219200-22221400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:22219200-22221400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:22219200-22221800	Weak transcription	Primary B cells from cord blood	blood
30	chr12:22219200-22222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:22219200-22223000	Weak transcription	Placenta	Placenta
32	chr12:22219400-22221200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:22219400-22221200	Weak transcription	HMEC	breast
34	chr12:22219400-22221400	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:22219400-22221800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:22219400-22222800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:22219600-22221200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:22219600-22221200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:22219600-22221200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:22219600-22221200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:22219600-22221200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:22219600-22221400	Weak transcription	Dnd41	blood
43	chr12:22219600-22221600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:22219600-22222200	Weak transcription	Brain Anterior Caudate	brain
45	chr12:22219600-22224200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:22219800-22221400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:22219800-22221400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:22219800-22221400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:22219800-22221400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:22219800-22221400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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