Variant report

Variant	rs4802770
Chromosome Location	chr19:39223402-39223403
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1136956	0.82[EUR][1000 genomes]
rs12986332	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	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
2	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
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4802770	ENSG00000182472	cis	multi-tissue	Pritchard
rs4802770	CAPN12	Cis_1M	lymphoblastoid	RTeQTL
rs4802770	CAPN12	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39211200-39224000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:39213200-39223600	Strong transcription	HSMMtube	muscle
4	chr19:39213400-39223600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39213400-39224400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:39213800-39223600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:39213800-39224400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:39214000-39224800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:39214400-39224000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:39215600-39224000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:39215600-39224800	Genic enhancers	A549	lung
12	chr19:39216200-39223800	Weak transcription	Fetal Thymus	thymus
13	chr19:39217000-39224400	Genic enhancers	Fetal Intestine Large	intestine
14	chr19:39217200-39224400	Genic enhancers	Fetal Intestine Small	intestine
15	chr19:39217800-39224200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39217800-39224200	Weak transcription	GM12878-XiMat	blood
17	chr19:39218000-39225000	Weak transcription	Primary T cells from cord blood	blood
18	chr19:39218000-39226800	Weak transcription	Psoas Muscle	Psoas
19	chr19:39218400-39224600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:39218600-39225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:39218800-39225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:39218800-39226600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:39219000-39223800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:39219000-39224000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:39219400-39224600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:39220000-39223600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:39220000-39224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39220800-39223800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:39220800-39224600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:39220800-39226800	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:39221200-39224000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:39221200-39225400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:39221200-39226000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:39221600-39224000	Weak transcription	NHDF-Ad	bronchial
35	chr19:39221800-39223600	Genic enhancers	Gastric	stomach
36	chr19:39221800-39224000	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr19:39221800-39224000	Genic enhancers	HMEC	breast
38	chr19:39221800-39224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:39222000-39223600	Genic enhancers	Placenta	Placenta
40	chr19:39222000-39223800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:39222000-39224200	Weak transcription	Small Intestine	intestine
42	chr19:39222000-39225200	Enhancers	Pancreas	Pancrea
43	chr19:39222200-39224200	Genic enhancers	Fetal Muscle Leg	muscle
44	chr19:39222200-39224800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr19:39222200-39225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:39222200-39226200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:39222200-39226800	Weak transcription	Brain Substantia Nigra	brain
48	chr19:39222400-39223800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:39222400-39224000	Weak transcription	Primary B cells from cord blood	blood
50	chr19:39222400-39224800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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