Variant report

Variant	rs10495216
Chromosome Location	chr1:223904595-223904596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223903451..223905300-chr1:223920938..223923297,2	MCF-7	breast:
2	chr1:223891592..223893967-chr1:223903233..223904840,2	K562	blood:
3	chr1:223903418..223905687-chr1:223928822..223931791,2	MCF-7	breast:
4	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
5	chr1:223904423..223906015-chr1:223946207..223948782,2	K562	blood:
6	chr1:223904247..223905976-chr1:223916920..223919197,2	MCF-7	breast:
7	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10495215	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503144	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12059770	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12066704	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12069561	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12080250	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12088254	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs1222138	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12563637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12566817	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12568612	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[JPT][hapmap]
rs16842162	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842257	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842326	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842343	1.00[JPT][hapmap]
rs17556570	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs28370026	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370031	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370032	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370043	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs4653522	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4993742	0.82[CEU][hapmap]
rs61823964	0.87[EUR][1000 genomes]
rs61823979	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6671245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678365	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6683052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6685557	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6691315	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693884	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6696053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6700366	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6703104	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7331	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs751609	0.85[CEU][hapmap]
rs7530328	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7533551	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7535882	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7549063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv437346	chr1:223903781-223905532	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10495216	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223900800-223906000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:223901000-223905200	Enhancers	Spleen	Spleen
3	chr1:223901000-223905800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:223901200-223904600	Enhancers	Small Intestine	intestine
5	chr1:223901200-223904800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:223901200-223905400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:223901400-223904800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
8	chr1:223901400-223905600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
10	chr1:223901600-223904600	Enhancers	Brain Hippocampus Middle	brain
11	chr1:223901600-223905200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr1:223901600-223905800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:223901800-223904600	Enhancers	Right Atrium	heart
16	chr1:223901800-223904800	Enhancers	Fetal Brain Female	brain
17	chr1:223901800-223905000	Enhancers	Fetal Heart	heart
18	chr1:223901800-223905000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:223901800-223905200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:223901800-223905600	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr1:223901800-223905800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:223901800-223906200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:223902000-223905000	Enhancers	Fetal Brain Male	brain
24	chr1:223902200-223904600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:223902200-223904800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:223902200-223904800	Genic enhancers	Fetal Stomach	stomach
27	chr1:223902200-223905200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:223902400-223905800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:223902400-223906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:223902400-223906600	Enhancers	Fetal Thymus	thymus
32	chr1:223902600-223904800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:223902600-223904800	Enhancers	Stomach Mucosa	stomach
34	chr1:223902600-223904800	Flanking Active TSS	HSMMtube	muscle
35	chr1:223902600-223905000	Enhancers	Gastric	stomach
36	chr1:223902600-223905000	Flanking Active TSS	GM12878-XiMat	blood
37	chr1:223902600-223905200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:223902600-223905400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:223902600-223906000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:223902800-223904800	Enhancers	Psoas Muscle	Psoas
41	chr1:223902800-223905000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:223903000-223905000	Genic enhancers	Colon Smooth Muscle	Colon
44	chr1:223903000-223905800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:223903000-223906000	Enhancers	Primary B cells from cord blood	blood
46	chr1:223903000-223907800	Weak transcription	Liver	Liver
47	chr1:223903200-223904600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
48	chr1:223903200-223906400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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