Variant report

Variant	rs3213316
Chromosome Location	chr19:44066672-44066673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr19:44066585-44067274	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:44066656-44067392	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:44066659-44067412	U87	brain:	n/a	n/a
4	POLR2A	chr19:44066335-44067427	HL-60	blood:	n/a	n/a
5	POLR2A	chr19:44066339-44067427	HL-60	blood:	n/a	n/a
6	BCLAF1	chr19:44066652-44067305	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:44066659-44067394	U87	brain:	n/a	n/a
8	FOXM1	chr19:44066628-44067193	GM12878	blood:	n/a	n/a
9	MAX	chr19:44066566-44067428	NB4	blood:	n/a	n/a
10	POLR2A	chr19:44066633-44067349	U87	brain:	n/a	n/a
11	MTA3	chr19:44066362-44067421	GM12878	blood:	n/a	n/a
12	RCOR1	chr19:44066360-44067438	IMR90	lung:	n/a	n/a
13	BCLAF1	chr19:44066657-44067132	GM12878	blood:	n/a	n/a
14	RUNX3	chr19:44066602-44067385	GM12878	blood:	n/a	n/a
15	MEF2A	chr19:44066622-44067358	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44065179..44067890-chr19:44122794..44124973,2	K562	blood:
2	chr19:44063536..44067996-chr19:44097389..44100718,5	MCF-7	breast:
3	chr19:44065444..44067870-chr19:44076256..44078138,2	MCF-7	breast:

No data

Variant related genes	Relation type
XRCC1	TF binding region
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000131116	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs168310	1.00[ASN][1000 genomes]
rs2854497	1.00[ASN][1000 genomes]
rs3213293	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs3213321	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213339	0.82[AMR][1000 genomes]
rs3213348	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34439296	1.00[ASN][1000 genomes]
rs34471331	1.00[ASN][1000 genomes]
rs346049	1.00[ASN][1000 genomes]
rs399300	1.00[ASN][1000 genomes]
rs4251895	1.00[ASN][1000 genomes]
rs4251915	1.00[ASN][1000 genomes]
rs56204051	1.00[ASN][1000 genomes]
rs57817750	1.00[ASN][1000 genomes]
rs60175550	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60273962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60889018	1.00[ASN][1000 genomes]
rs7257640	1.00[ASN][1000 genomes]
rs73554667	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73554679	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73554696	1.00[ASN][1000 genomes]
rs73556510	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73556512	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73556542	1.00[AFR][1000 genomes]
rs73556565	1.00[ASN][1000 genomes]
rs73556581	1.00[ASN][1000 genomes]
rs8104645	1.00[ASN][1000 genomes]
rs8110767	0.86[AFR][1000 genomes];1.00[ASN][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	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
2	chr19:44043800-44074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:44044600-44069000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44048200-44067000	Weak transcription	HUVEC	blood vessel
5	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
6	chr19:44052800-44068400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:44053400-44068800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:44053400-44069400	Strong transcription	Fetal Stomach	stomach
9	chr19:44053600-44068600	Strong transcription	Fetal Intestine Large	intestine
10	chr19:44057200-44067000	Weak transcription	Fetal Brain Male	brain
11	chr19:44057600-44071200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
13	chr19:44058400-44071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:44059000-44076000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:44059200-44066800	Weak transcription	HMEC	breast
17	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:44061800-44069000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:44062400-44067400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:44062400-44067400	Strong transcription	Fetal Brain Female	brain
22	chr19:44062600-44076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:44063200-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:44063400-44067400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:44063400-44076200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:44063600-44069200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:44063800-44067000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:44063800-44067200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:44063800-44067200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:44063800-44068600	Strong transcription	Fetal Lung	lung
31	chr19:44063800-44069200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:44064400-44067000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:44064600-44068800	Strong transcription	HepG2	liver
34	chr19:44064800-44067000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:44064800-44068000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:44064800-44068600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:44064800-44069600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:44065000-44067200	Strong transcription	Fetal Kidney	kidney
39	chr19:44065000-44067800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:44065000-44068800	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:44065200-44067200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:44065200-44068400	Strong transcription	A549	lung
43	chr19:44065200-44068600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:44065200-44078600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:44065400-44066800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:44065400-44067000	Genic enhancers	Dnd41	blood
47	chr19:44065400-44069400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:44065400-44069600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:44065400-44078600	Weak transcription	Ovary	ovary
50	chr19:44065400-44078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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