Variant report

Variant	rs1222142
Chromosome Location	chr1:223925627-223925628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223919205..223921124-chr1:223921422..223926352,4	K562	blood:
2	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
3	chr1:223924785..223927259-chr1:223936900..223938830,2	K562	blood:
4	chr1:223906912..223908483-chr1:223923323..223925771,2	MCF-7	breast:
5	chr1:223925259..223927259-chr1:223937310..223938830,2	K562	blood:
6	chr1:223924368..223926769-chr1:223968941..223970904,2	K562	blood:
7	chr1:223898969..223903164-chr1:223924094..223928992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10915702	0.88[EUR][1000 genomes]
rs10915707	0.85[EUR][1000 genomes]
rs10915715	0.83[EUR][1000 genomes]
rs12022934	0.85[ASN][1000 genomes]
rs12023822	0.85[ASN][1000 genomes]
rs12037507	0.85[ASN][1000 genomes]
rs12046438	0.85[ASN][1000 genomes]
rs12066704	0.88[EUR][1000 genomes]
rs12066829	0.88[EUR][1000 genomes]
rs12066831	0.88[EUR][1000 genomes]
rs12069561	0.85[EUR][1000 genomes]
rs12070057	0.88[EUR][1000 genomes]
rs12080250	0.80[EUR][1000 genomes]
rs1222134	0.85[EUR][1000 genomes]
rs1222138	0.87[EUR][1000 genomes]
rs1222140	0.91[EUR][1000 genomes]
rs1222141	0.91[EUR][1000 genomes]
rs12562109	0.85[EUR][1000 genomes]
rs12563291	0.85[EUR][1000 genomes]
rs12563477	0.80[EUR][1000 genomes]
rs12563637	0.88[EUR][1000 genomes]
rs12563713	0.84[EUR][1000 genomes]
rs16842162	0.80[EUR][1000 genomes]
rs17557525	0.83[EUR][1000 genomes]
rs17557623	0.83[EUR][1000 genomes]
rs17597	0.85[EUR][1000 genomes]
rs17598	0.85[EUR][1000 genomes]
rs17600	0.85[EUR][1000 genomes]
rs28370026	0.83[EUR][1000 genomes]
rs28370031	0.83[EUR][1000 genomes]
rs28370032	0.83[EUR][1000 genomes]
rs28370041	0.85[ASN][1000 genomes]
rs28370043	0.84[EUR][1000 genomes]
rs28370069	0.81[EUR][1000 genomes]
rs28370170	0.80[EUR][1000 genomes]
rs3738373	0.85[EUR][1000 genomes]
rs3738374	0.85[EUR][1000 genomes]
rs3738375	0.85[EUR][1000 genomes]
rs3767716	0.84[EUR][1000 genomes]
rs3767717	0.85[EUR][1000 genomes]
rs3767718	0.85[EUR][1000 genomes]
rs59206866	0.83[ASN][1000 genomes]
rs59248553	0.88[EUR][1000 genomes]
rs59275322	0.91[EUR][1000 genomes]
rs61823979	0.80[EUR][1000 genomes]
rs61824003	0.80[EUR][1000 genomes]
rs6665485	0.84[EUR][1000 genomes]
rs6671245	0.83[EUR][1000 genomes]
rs6674541	0.83[EUR][1000 genomes]
rs6674846	0.83[EUR][1000 genomes]
rs6683052	0.83[EUR][1000 genomes]
rs6685475	0.83[EUR][1000 genomes]
rs6693372	0.80[EUR][1000 genomes]
rs6693884	0.83[EUR][1000 genomes]
rs7331	0.80[EUR][1000 genomes]
rs751609	0.88[EUR][1000 genomes]
rs7549063	0.83[EUR][1000 genomes]
rs7555226	0.91[EUR][1000 genomes]
rs898876	0.88[EUR][1000 genomes]
rs898877	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1222142	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223915400-223927200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:223916600-223927000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
9	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:223919800-223926000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:223919800-223931200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:223921200-223927800	Genic enhancers	A549	lung
14	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:223921400-223926000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:223921600-223926000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:223921600-223926000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:223921600-223926200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:223921600-223932800	Weak transcription	Liver	Liver
22	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:223921800-223926000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:223922200-223925800	Weak transcription	Fetal Kidney	kidney
28	chr1:223922200-223926200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:223922200-223926400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
32	chr1:223922400-223926200	Weak transcription	NHDF-Ad	bronchial
33	chr1:223922400-223926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:223922400-223927400	Weak transcription	Small Intestine	intestine
35	chr1:223922400-223927800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:223922600-223926200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:223922600-223927200	Weak transcription	Fetal Lung	lung
38	chr1:223922600-223927200	Weak transcription	K562	blood
39	chr1:223922600-223928000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:223922800-223925800	Weak transcription	Fetal Intestine Large	intestine
41	chr1:223922800-223926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:223922800-223926200	Weak transcription	Fetal Heart	heart
43	chr1:223922800-223926200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:223922800-223927200	Weak transcription	Psoas Muscle	Psoas
45	chr1:223922800-223928600	Weak transcription	Fetal Thymus	thymus
46	chr1:223922800-223930600	Weak transcription	Spleen	Spleen
47	chr1:223922800-223930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:223922800-223931600	Weak transcription	Brain Germinal Matrix	brain
49	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:223923000-223926000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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