Variant report

Variant	rs17665451
Chromosome Location	chr19:39153307-39153308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
2	chr19:39151862..39154243-chr19:39220891..39223454,2	MCF-7	breast:
3	chr19:39151900..39153408-chr19:39203433..39205156,2	MCF-7	breast:
4	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
5	chr19:39136583..39139247-chr19:39152891..39155036,2	K562	blood:
6	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
7	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
8	chr19:39151502..39153525-chr19:39175124..39177403,2	MCF-7	breast:
9	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
10	chr19:39152968..39155649-chr19:39189504..39191382,2	MCF-7	breast:
11	chr19:39151359..39154098-chr19:39320807..39323487,3	MCF-7	breast:
12	chr19:39152027..39154763-chr19:39201126..39202967,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11553600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17589415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17708009	1.00[CHB][hapmap]
rs2228068	1.00[CHB][hapmap]
rs41482151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45468197	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4801859	0.85[CEU][hapmap]
rs4802744	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4802747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802775	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67438539	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7246615	0.91[YRI][hapmap]
rs7258075	1.00[CHB][hapmap]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73032691	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73032697	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034621	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.90[EUR][1000 genomes]
rs73038936	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038948	1.00[ASN][1000 genomes]
rs7351086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888995	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[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	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17665451	CAPN12	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr19:39144200-39153400	Genic enhancers	K562	blood
4	chr19:39144600-39154000	Enhancers	Right Atrium	heart
5	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
6	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
7	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
10	chr19:39147800-39160800	Enhancers	Placenta	Placenta
11	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
12	chr19:39149000-39154200	Enhancers	Brain Substantia Nigra	brain
13	chr19:39149000-39154600	Weak transcription	Primary T cells from cord blood	blood
14	chr19:39149000-39155200	Weak transcription	Fetal Brain Female	brain
15	chr19:39149200-39153400	Genic enhancers	Fetal Muscle Leg	muscle
16	chr19:39149600-39154000	Enhancers	Brain Hippocampus Middle	brain
17	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
18	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
19	chr19:39150200-39154200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr19:39150400-39153600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr19:39150400-39154400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:39150400-39155000	Genic enhancers	HMEC	breast
23	chr19:39150600-39154600	Genic enhancers	Osteobl	bone
24	chr19:39150800-39154400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:39150800-39155000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:39151000-39154400	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr19:39151000-39154600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:39151200-39154800	Genic enhancers	HepG2	liver
29	chr19:39151200-39155800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
32	chr19:39151400-39154400	Genic enhancers	HSMM	muscle
33	chr19:39151400-39155200	Genic enhancers	HSMMtube	muscle
34	chr19:39151400-39156200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:39151400-39157400	Genic enhancers	NHLF	lung
36	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr19:39151600-39153400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:39151600-39153400	Transcr. at gene 5' and 3'	NHEK	skin
39	chr19:39151600-39154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:39151600-39154200	Enhancers	Brain Anterior Caudate	brain
41	chr19:39151800-39156800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:39152000-39153400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:39152000-39153400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:39152000-39153600	Enhancers	Fetal Kidney	kidney
45	chr19:39152000-39153600	Enhancers	Small Intestine	intestine
46	chr19:39152000-39154000	Enhancers	Adipose Nuclei	Adipose
47	chr19:39152000-39154000	Enhancers	Left Ventricle	heart
48	chr19:39152000-39154000	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr19:39152000-39154200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr19:39152000-39154600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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