Variant report

Variant	rs25496
Chromosome Location	chr19:44065102-44065103
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	CTCF	chr19:44064830-44065109	MCF-7	breast:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
2	ZMIZ1	chr19:44064893-44065191	K562	blood:	n/a	n/a
3	FOSL2	chr19:44064763-44065217	A549	lung:	n/a	chr19:44064952-44064961
4	JUND	chr19:44064767-44065171	K562	blood:	n/a	chr19:44064951-44064962 chr19:44064952-44064961
5	CTCF	chr19:44064752-44065212	MCF-7	breast:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
6	JUND	chr19:44064828-44065118	H1-hESC	embryonic stem cell:	n/a	chr19:44064951-44064962 chr19:44064952-44064961
7	MAX	chr19:44064718-44065132	K562	blood:	n/a	n/a
8	POLR2A	chr19:44064858-44065150	K562	blood:	n/a	n/a
9	MAZ	chr19:44064799-44065116	K562	blood:	n/a	n/a
10	CTCF	chr19:44064817-44065171	K562	blood:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
11	CTCF	chr19:44064775-44065105	H1-hESC	embryonic stem cell:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
12	CTCF	chr19:44064698-44065212	MCF-7	breast:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
13	FOSL1	chr19:44064762-44065110	K562	blood:	n/a	chr19:44064952-44064961
14	CTCF	chr19:44064760-44065156	K562	blood:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
15	CTCF	chr19:44064815-44065129	H1-hESC	embryonic stem cell:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
16	MAZ	chr19:44064776-44065105	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr19:44064775-44065110	GM12878	blood:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
18	RAD21	chr19:44064689-44065152	H1-hESC	embryonic stem cell:	n/a	chr19:44064931-44064944 chr19:44064928-44064947 chr19:44064933-44064943 chr19:44064933-44064945
19	JUN	chr19:44064789-44065115	K562	blood:	n/a	chr19:44064952-44064961
20	RAD21	chr19:44064827-44065108	H1-hESC	embryonic stem cell:	n/a	chr19:44064931-44064944 chr19:44064928-44064947 chr19:44064933-44064943 chr19:44064933-44064945
21	POLR2A	chr19:44064713-44065127	GM12892	blood:	n/a	n/a
22	RAD21	chr19:44064739-44065145	HepG2	liver:	n/a	chr19:44064931-44064944 chr19:44064928-44064947 chr19:44064933-44064943 chr19:44064933-44064945
23	CTCF	chr19:44064816-44065259	K562	blood:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
24	CTCF	chr19:44064799-44065117	K562	blood:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
25	RAD21	chr19:44064713-44065181	MCF-7	breast:	n/a	chr19:44064931-44064944 chr19:44064928-44064947 chr19:44064933-44064943 chr19:44064933-44064945
26	CREB1	chr19:44064829-44065169	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOSL2	chr19:44064699-44065240	MCF-7	breast:	n/a	chr19:44064952-44064961
28	CTCF	chr19:44064570-44065189	A549	lung:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
29	CTCF	chr19:44064834-44065117	Fibrobl	skin:	n/a	chr19:44064927-44064945 chr19:44064930-44064943 chr19:44064989-44064998
30	CTCF	chr19:44064960-44065110	GM12875	blood:	n/a	chr19:44064989-44064998
31	MAX	chr19:44064903-44065111	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44063536..44067996-chr19:44097389..44100718,5	MCF-7	breast:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3213242	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213254	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213274	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs3213309	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213380	1.00[AMR][1000 genomes]
rs73935005	1.00[AMR][1000 genomes]
rs9653099	1.00[AMR][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	chr19:44041800-44065200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:44043600-44065800	Strong transcription	Adipose Nuclei	Adipose
4	chr19:44043800-44065800	Weak transcription	Fetal Heart	heart
5	chr19:44043800-44074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:44044600-44069000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:44047400-44066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:44048200-44067000	Weak transcription	HUVEC	blood vessel
9	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
10	chr19:44052800-44068400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:44053000-44065600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:44053000-44066200	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:44053400-44068800	Strong transcription	Fetal Intestine Small	intestine
14	chr19:44053400-44069400	Strong transcription	Fetal Stomach	stomach
15	chr19:44053600-44068600	Strong transcription	Fetal Intestine Large	intestine
16	chr19:44054000-44065600	Strong transcription	Placenta	Placenta
17	chr19:44056000-44066600	Weak transcription	Psoas Muscle	Psoas
18	chr19:44056400-44066400	Weak transcription	Stomach Mucosa	stomach
19	chr19:44057200-44067000	Weak transcription	Fetal Brain Male	brain
20	chr19:44057600-44071200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
22	chr19:44058400-44071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:44059000-44076000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:44059200-44066600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:44059200-44066800	Weak transcription	HMEC	breast
27	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:44059400-44065200	Weak transcription	A549	lung
29	chr19:44059400-44066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:44059800-44065200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:44059800-44066600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:44060400-44065800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:44060400-44066600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:44061600-44065400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr19:44061800-44069000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:44062400-44065200	Weak transcription	NH-A	brain
38	chr19:44062400-44066400	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:44062400-44067400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:44062400-44067400	Strong transcription	Fetal Brain Female	brain
41	chr19:44062600-44066600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:44062600-44076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:44062800-44066400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:44063200-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:44063400-44065400	Strong transcription	Brain Anterior Caudate	brain
46	chr19:44063400-44067400	Strong transcription	Brain Germinal Matrix	brain
47	chr19:44063400-44076200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:44063600-44065200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:44063600-44065800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:44063600-44065800	Strong transcription	Liver	Liver

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