Variant report

Variant	rs45468197
Chromosome Location	chr19:39225858-39225859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39223740-39225954	U87	brain:	n/a	n/a
2	SIN3AK20	chr19:39223100-39226358	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39223292-39226313	MCF-7	breast:	n/a	n/a
4	PBX3	chr19:39223832-39226377	A549	lung:	n/a	n/a
5	MAX	chr19:39225751-39226368	A549	lung:	n/a	n/a
6	JUND	chr19:39223167-39226365	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
7	REST	chr19:39224502-39226286	A549	lung:	n/a	n/a
8	ZBTB7A	chr19:39225521-39226387	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr19:39221228-39226317	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:39224879-39225887	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:39223643-39226161	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr19:39223236-39226266	HepG2	liver:	n/a	n/a
13	SP1	chr19:39224912-39226374	A549	lung:	n/a	chr19:39225419-39225433 chr19:39226104-39226113 chr19:39224924-39224938 chr19:39226104-39226113 chr19:39225426-39225440 chr19:39226103-39226114 chr19:39225939-39225953 chr19:39226105-39226114
14	MAX	chr19:39225856-39226316	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr19:39225827-39226284	K562	blood:	n/a	n/a
16	MAX	chr19:39223136-39226382	A549	lung:	n/a	chr19:39225279-39225290 chr19:39225280-39225289 chr19:39224434-39224443
17	POLR2A	chr19:39223909-39226321	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr19:39225780-39225930	GM12873	blood:	n/a	n/a
19	SIX5	chr19:39223165-39226400	A549	lung:	n/a	chr19:39223670-39223684
20	EP300	chr19:39224505-39226255	A549	lung:	n/a	n/a
21	SP1	chr19:39224887-39226381	A549	lung:	n/a	chr19:39225419-39225433 chr19:39226104-39226113 chr19:39224924-39224938 chr19:39226104-39226113 chr19:39225426-39225440 chr19:39226103-39226114 chr19:39225939-39225953 chr19:39226105-39226114
22	ATF3	chr19:39225805-39226334	A549	lung:	n/a	n/a
23	FOSL2	chr19:39223785-39226303	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
24	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
25	ZBTB33	chr19:39224013-39226329	A549	lung:	n/a	n/a
26	POLR2A	chr19:39221828-39226356	U87	brain:	n/a	n/a
27	ELF1	chr19:39224736-39226313	GM12878	blood:	n/a	chr19:39225057-39225070
28	ZNF143	chr19:39225835-39225930	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:39224747-39226348	A549	lung:	n/a	n/a
30	POLR2A	chr19:39223737-39226322	A549	lung:	n/a	n/a
31	ZBTB7A	chr19:39225325-39226322	K562	blood:	n/a	n/a
32	ZBTB7A	chr19:39225129-39226373	ECC-1	luminal epithelium:	n/a	n/a
33	YY1	chr19:39225663-39226305	A549	lung:	n/a	n/a
34	CREB1	chr19:39225652-39226183	A549	lung:	n/a	n/a
35	POLR2A	chr19:39224913-39225932	SK-N-SH	brain:	n/a	n/a
36	SIN3AK20	chr19:39225007-39226309	A549	lung:	n/a	n/a
37	POLR2A	chr19:39220891-39226327	K562	blood:	n/a	n/a
38	BCL3	chr19:39223165-39226356	A549	lung:	n/a	chr19:39225058-39225067
39	BCL3	chr19:39221661-39226381	A549	lung:	n/a	chr19:39222655-39222664 chr19:39225058-39225067
40	POLR2A	chr19:39221895-39226350	U87	brain:	n/a	n/a
41	TCF12	chr19:39223129-39226326	A549	lung:	n/a	chr19:39225425-39225435
42	PBX3	chr19:39224126-39226368	A549	lung:	n/a	n/a
43	POLR2A	chr19:39223288-39226331	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:39223210-39226316	A549	lung:	n/a	n/a
45	REST	chr19:39224929-39226333	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr19:39220818-39226344	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr19:39223743-39225954	U87	brain:	n/a	n/a
48	POLR2A	chr19:39225826-39225972	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:39224904-39226301	H1-hESC	embryonic stem cell:	n/a	n/a
50	ELF1	chr19:39225679-39226339	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39224374..39227247-chr19:39227661..39229256,2	MCF-7	breast:
2	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
3	chr19:39225035..39229236-chr19:39320225..39324035,5	K562	blood:
4	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
5	chr19:39224613..39228237-chr19:39319464..39324480,6	MCF-7	breast:
6	chr19:39225241..39228879-chr19:39342547..39344492,3	K562	blood:
7	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
8	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
9	chr19:39223964..39228282-chr19:39327392..39332302,8	MCF-7	breast:
10	chr19:39138420..39142103-chr19:39224990..39229224,5	MCF-7	breast:
11	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGALS7-1	chr19:39223761-39226312	NONHSAT066236

Variant related genes	Relation type
ENSG00000267892	TF binding region
ENSG00000267892	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104823	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11553600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	1.00[ASN][1000 genomes]
rs17589415	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665451	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41482151	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[ASN][1000 genomes]
rs4802747	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802775	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438539	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	1.00[ASN][1000 genomes]
rs73032691	1.00[ASN][1000 genomes]
rs73032697	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034621	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73038936	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038948	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351086	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888995	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	esv3421629	chr19:39225537-39228485	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3360199	chr19:39225562-39228860	Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3437673	chr19:39225662-39228610	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45468197	CAPN12	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39218000-39226800	Weak transcription	Psoas Muscle	Psoas
2	chr19:39218800-39226600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39220800-39226800	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:39221200-39226000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:39222200-39226200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr19:39222200-39226800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:39222400-39226200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39222400-39226600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:39222400-39226800	Weak transcription	Brain Angular Gyrus	brain
10	chr19:39222400-39226800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:39222600-39226800	Weak transcription	Fetal Heart	heart
12	chr19:39222600-39227200	Weak transcription	Fetal Kidney	kidney
13	chr19:39222800-39226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:39222800-39226600	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:39222800-39226800	Weak transcription	Brain Anterior Caudate	brain
16	chr19:39222800-39226800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:39222800-39227400	Weak transcription	Aorta	Aorta
18	chr19:39223000-39226600	Enhancers	Right Ventricle	heart
19	chr19:39223200-39226800	Enhancers	Adipose Nuclei	Adipose
20	chr19:39223400-39226000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr19:39223600-39226000	Enhancers	Liver	Liver
22	chr19:39223600-39226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:39223600-39226600	Weak transcription	Ovary	ovary
24	chr19:39223600-39227200	Weak transcription	Fetal Lung	lung
25	chr19:39223800-39226000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr19:39223800-39226200	Enhancers	HUVEC	blood vessel
27	chr19:39223800-39227400	Enhancers	HSMM	muscle
28	chr19:39224000-39226000	Enhancers	HMEC	breast
29	chr19:39224000-39226400	Enhancers	Hela-S3	cervix
30	chr19:39224000-39226600	Weak transcription	Right Atrium	heart
31	chr19:39224000-39226800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:39224000-39226800	Enhancers	Fetal Muscle Trunk	muscle
33	chr19:39224000-39227000	Enhancers	NH-A	brain
34	chr19:39224200-39226400	Enhancers	HepG2	liver
35	chr19:39224200-39226600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:39224200-39226600	Enhancers	Fetal Muscle Leg	muscle
37	chr19:39224200-39227000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:39224400-39226000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr19:39224400-39226200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
40	chr19:39224400-39226400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:39224400-39226800	Weak transcription	Left Ventricle	heart
42	chr19:39224600-39226200	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr19:39224600-39226200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr19:39224600-39226400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39224800-39226200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr19:39224800-39226200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:39224800-39226200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr19:39224800-39226200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr19:39224800-39226200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr19:39224800-39226400	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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