Variant report

Variant	rs557121788
Chromosome Location	chr19:39226081-39226082
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	SIN3AK20	chr19:39223100-39226358	PANC-1	pancreas:	n/a	n/a
2	SP4	chr19:39226022-39226378	H1-hESC	embryonic stem cell:	n/a	chr19:39226103-39226114
3	POLR2A	chr19:39223292-39226313	MCF-7	breast:	n/a	n/a
4	ETS1	chr19:39225877-39226281	A549	lung:	n/a	chr19:39225945-39225958
5	PBX3	chr19:39223832-39226377	A549	lung:	n/a	n/a
6	MAX	chr19:39225751-39226368	A549	lung:	n/a	n/a
7	JUND	chr19:39223167-39226365	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
8	REST	chr19:39224502-39226286	A549	lung:	n/a	n/a
9	MAZ	chr19:39226057-39226321	GM12878	blood:	n/a	n/a
10	GABPA	chr19:39225862-39226237	A549	lung:	n/a	n/a
11	ZBTB7A	chr19:39225521-39226387	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3AK20	chr19:39225902-39226124	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr19:39221228-39226317	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:39223643-39226161	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr19:39223236-39226266	HepG2	liver:	n/a	n/a
16	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
17	MAX	chr19:39225856-39226316	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr19:39225827-39226284	K562	blood:	n/a	n/a
19	BACH1	chr19:39226073-39226287	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD2	chr19:39225981-39226175	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr19:39223136-39226382	A549	lung:	n/a	chr19:39225279-39225290 chr19:39225280-39225289 chr19:39224434-39224443
22	POLR2A	chr19:39223909-39226321	ECC-1	luminal epithelium:	n/a	n/a
23	SIX5	chr19:39223165-39226400	A549	lung:	n/a	chr19:39223670-39223684
24	EP300	chr19:39224505-39226255	A549	lung:	n/a	n/a
25	SP1	chr19:39225920-39226348	H1-hESC	embryonic stem cell:	n/a	chr19:39226104-39226113 chr19:39226104-39226113 chr19:39226103-39226114 chr19:39225939-39225953 chr19:39226105-39226114
26	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
27	MXI1	chr19:39225933-39226107	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:39226004-39226299	HUVEC	blood vessel:	n/a	n/a
29	SIN3AK20	chr19:39225881-39226295	A549	lung:	n/a	n/a
30	ATF3	chr19:39225805-39226334	A549	lung:	n/a	n/a
31	ELF1	chr19:39225915-39226290	K562	blood:	n/a	n/a
32	FOSL2	chr19:39223785-39226303	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
33	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
34	SP1	chr19:39226053-39226340	GM12878	blood:	n/a	chr19:39226104-39226113 chr19:39226104-39226113 chr19:39226103-39226114 chr19:39226105-39226114
35	ZBTB33	chr19:39224013-39226329	A549	lung:	n/a	n/a
36	POLR2A	chr19:39221828-39226356	U87	brain:	n/a	n/a
37	ZBTB7A	chr19:39225867-39226313	K562	blood:	n/a	n/a
38	ELF1	chr19:39224736-39226313	GM12878	blood:	n/a	chr19:39225057-39225070
39	POLR2A	chr19:39224747-39226348	A549	lung:	n/a	n/a
40	POLR2A	chr19:39223737-39226322	A549	lung:	n/a	n/a
41	SIN3A	chr19:39225901-39226272	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZBTB7A	chr19:39225325-39226322	K562	blood:	n/a	n/a
43	YY1	chr19:39226002-39226157	K562	blood:	n/a	n/a
44	IRF1	chr19:39225905-39226385	K562	blood:	n/a	chr19:39226200-39226209
45	HMGN3	chr19:39226019-39226240	K562	blood:	n/a	n/a
46	ZBTB7A	chr19:39225129-39226373	ECC-1	luminal epithelium:	n/a	n/a
47	YY1	chr19:39225663-39226305	A549	lung:	n/a	n/a
48	CREB1	chr19:39225652-39226183	A549	lung:	n/a	n/a
49	SIN3AK20	chr19:39225007-39226309	A549	lung:	n/a	n/a
50	TCF12	chr19:39225930-39226312	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
CAPN12	TF binding region
ENSG00000267892	TF binding region
ENSG00000267892	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

No data

Chromatin state (count:119 , 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	chr19:39222200-39226200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr19:39222200-39226800	Weak transcription	Brain Substantia Nigra	brain
6	chr19:39222400-39226200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39222400-39226600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:39222400-39226800	Weak transcription	Brain Angular Gyrus	brain
9	chr19:39222400-39226800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39222600-39226800	Weak transcription	Fetal Heart	heart
11	chr19:39222600-39227200	Weak transcription	Fetal Kidney	kidney
12	chr19:39222800-39226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:39222800-39226600	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:39222800-39226800	Weak transcription	Brain Anterior Caudate	brain
15	chr19:39222800-39226800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:39222800-39227400	Weak transcription	Aorta	Aorta
17	chr19:39223000-39226600	Enhancers	Right Ventricle	heart
18	chr19:39223200-39226800	Enhancers	Adipose Nuclei	Adipose
19	chr19:39223600-39226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:39223600-39226600	Weak transcription	Ovary	ovary
21	chr19:39223600-39227200	Weak transcription	Fetal Lung	lung
22	chr19:39223800-39226200	Enhancers	HUVEC	blood vessel
23	chr19:39223800-39227400	Enhancers	HSMM	muscle
24	chr19:39224000-39226400	Enhancers	Hela-S3	cervix
25	chr19:39224000-39226600	Weak transcription	Right Atrium	heart
26	chr19:39224000-39226800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:39224000-39226800	Enhancers	Fetal Muscle Trunk	muscle
28	chr19:39224000-39227000	Enhancers	NH-A	brain
29	chr19:39224200-39226400	Enhancers	HepG2	liver
30	chr19:39224200-39226600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39224200-39226600	Enhancers	Fetal Muscle Leg	muscle
32	chr19:39224200-39227000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr19:39224400-39226200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
34	chr19:39224400-39226400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:39224400-39226800	Weak transcription	Left Ventricle	heart
36	chr19:39224600-39226200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr19:39224600-39226200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr19:39224600-39226400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:39224800-39226200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr19:39224800-39226200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:39224800-39226200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr19:39224800-39226200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:39224800-39226200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr19:39224800-39226400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr19:39225000-39226200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr19:39225000-39226200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr19:39225000-39226200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr19:39225000-39226200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:39225000-39226200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr19:39225000-39226200	Bivalent Enhancer	Fetal Thymus	thymus

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