Variant report

Variant	rs73937427
Chromosome Location	chr19:43969532-43969533
allele	A/C
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	TFAP2A	chr19:43969460-43970291	Hela-S3	cervix:	n/a	chr19:43969810-43969820 chr19:43969810-43969820 chr19:43969810-43969820 chr19:43969810-43969820 chr19:43969808-43969822 chr19:43969806-43969821 chr19:43969808-43969822
2	FOSL2	chr19:43969445-43970079	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:43969463-43970014	Hela-S3	cervix:	n/a	n/a
4	JUND	chr19:43969390-43970112	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:43969454-43969987	ProgFib	skin:	n/a	n/a
6	POLR2A	chr19:43969517-43969978	Hela-S3	cervix:	n/a	n/a
7	TFAP2C	chr19:43969443-43970491	Hela-S3	cervix:	n/a	chr19:43969806-43969821
8	POLR2A	chr19:43969531-43969933	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:43969494-43969836	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:43969342-43970091	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:43969352-43970179	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:43969275-43970101	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr19:43969394-43970544	MCF-7	breast:	n/a	n/a
14	PML	chr19:43969513-43969932	MCF-7	breast:	n/a	chr19:43969562-43969570
15	POLR2A	chr19:43969380-43970047	MCF-7	breast:	n/a	n/a
16	SMARCC1	chr19:43969398-43970462	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:43969359-43970108	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:43969157..43969660-chr3:15751924..15752424,2	Hela-S3	cervix:
2	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
3	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
4	chr19:43857729..43859549-chr19:43967499..43969532,2	MCF-7	breast:
5	chr19:43968715..43971429-chr19:44172597..44174445,2	MCF-7	breast:
6	chr19:43967717..43971076-chr19:44036987..44039699,3	MCF-7	breast:
7	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:

Variant related genes	Relation type
LYPD3	TF binding region
ENSG00000011422	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000204936	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11083710	1.00[EUR][1000 genomes]
rs11879973	1.00[EUR][1000 genomes]
rs55908340	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56284822	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56296628	1.00[EUR][1000 genomes]
rs59051447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61732260	1.00[EUR][1000 genomes]
rs73935005	1.00[EUR][1000 genomes]
rs73935006	1.00[EUR][1000 genomes]
rs73937413	1.00[EUR][1000 genomes]
rs73937428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9653099	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43967400-43970200	Active TSS	Esophagus	oesophagus
2	chr19:43968000-43970000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:43968000-43970000	Flanking Active TSS	Placenta	Placenta
4	chr19:43968400-43970000	Enhancers	Fetal Heart	heart
5	chr19:43968600-43969600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:43968600-43969800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:43968600-43970000	Enhancers	Gastric	stomach
8	chr19:43968600-43970200	Enhancers	Spleen	Spleen
9	chr19:43968600-43970400	Enhancers	Pancreas	Pancrea
10	chr19:43968600-43970400	Flanking Active TSS	Hela-S3	cervix
11	chr19:43968800-43969600	Weak transcription	Ovary	ovary
12	chr19:43968800-43969800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:43968800-43969800	Weak transcription	Lung	lung
14	chr19:43968800-43969800	Active TSS	Placenta Amnion	Placenta Amnion
15	chr19:43968800-43970000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:43968800-43970000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr19:43968800-43970200	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr19:43968800-43970200	Enhancers	NHDF-Ad	bronchial
19	chr19:43968800-43970400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr19:43968800-43970400	Bivalent Enhancer	Fetal Stomach	stomach
21	chr19:43968800-43970600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr19:43968800-43971400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:43968800-43979200	Weak transcription	Right Atrium	heart
24	chr19:43969000-43969600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr19:43969000-43969600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:43969000-43969600	Enhancers	Colonic Mucosa	Colon
27	chr19:43969000-43969600	Enhancers	Stomach Smooth Muscle	stomach
28	chr19:43969000-43969600	Enhancers	Dnd41	blood
29	chr19:43969000-43969800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr19:43969000-43969800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:43969000-43969800	Enhancers	Colon Smooth Muscle	Colon
32	chr19:43969000-43970000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr19:43969000-43970000	Enhancers	Primary T cells from cord blood	blood
34	chr19:43969000-43970000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:43969000-43970000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr19:43969000-43970200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:43969000-43970200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr19:43969000-43970200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:43969000-43970400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:43969000-43971400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:43969000-43971400	Weak transcription	K562	blood
42	chr19:43969000-43971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:43969000-43971600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:43969000-43971600	Weak transcription	Osteobl	bone
45	chr19:43969000-43971800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:43969000-43972000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:43969000-43972000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:43969000-43979000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:43969000-43979000	Weak transcription	A549	lung
50	chr19:43969200-43969600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links