Variant report

Variant	rs3213348
Chromosome Location	chr19:44059637-44059638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:44059304-44059690	HCT-116	colon:	n/a	n/a
2	SMC3	chr19:44059350-44059708	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr19:44059394-44059663	MCF-7	breast:	n/a	n/a
4	CTCF	chr19:44059385-44059649	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr19:44059187-44059675	MCF-7	breast:	n/a	n/a
6	MAFK	chr19:44059437-44059658	HepG2	liver:	n/a	n/a
7	ZEB1	chr19:44059301-44059643	GM12878	blood:	n/a	n/a
8	RAD21	chr19:44059336-44059749	HepG2	liver:	n/a	n/a
9	YY1	chr19:44059312-44059704	GM12878	blood:	n/a	n/a
10	SMC3	chr19:44058961-44059806	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr19:44059340-44059716	GM12878	blood:	n/a	n/a
12	RAD21	chr19:44059275-44059755	HepG2	liver:	n/a	n/a
13	ZNF143	chr19:44059386-44059673	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:44059367-44059649	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF143	chr19:44059361-44059679	GM12878	blood:	n/a	n/a
16	CTCF	chr19:44059376-44059664	MCF-7	breast:	n/a	n/a
17	CTCF	chr19:44059373-44059683	GM12891	blood:	n/a	n/a
18	CTCF	chr19:44059368-44059644	GM13977	blood:	n/a	n/a
19	SMC3	chr19:44059305-44059706	HepG2	liver:	n/a	n/a
20	CTCF	chr19:44059141-44059867	A549	lung:	n/a	n/a
21	MTA3	chr19:44059341-44059704	GM12878	blood:	n/a	n/a
22	RCOR1	chr19:44059389-44059710	K562	blood:	n/a	n/a
23	RAD21	chr19:44059342-44059668	SK-N-SH_RA	brain:	n/a	n/a
24	RAD21	chr19:44059366-44059698	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:44059515-44059677	K562	blood:	n/a	n/a
26	CTCF	chr19:44059370-44059676	GM12892	blood:	n/a	n/a
27	CTCF	chr19:44059370-44059652	Medullo	brain:	n/a	n/a
28	CTCF	chr19:44059266-44059704	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:44059341-44059691	Spleen_OC	spleen:	n/a	n/a
30	SMC3	chr19:44059329-44059712	GM12878	blood:	n/a	n/a
31	RAD21	chr19:44059350-44059690	A549	lung:	n/a	n/a
32	CTCF	chr19:44059391-44059647	Fibrobl	skin:	n/a	n/a
33	RAD21	chr19:44059346-44059738	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr19:44059271-44059780	ECC-1	luminal epithelium:	n/a	n/a
35	JUND	chr19:44059374-44059652	K562	blood:	n/a	n/a
36	MYC	chr19:44059372-44059704	NB4	blood:	n/a	n/a
37	RUNX3	chr19:44059288-44059679	GM12878	blood:	n/a	n/a
38	CTCF	chr19:44059386-44059643	MCF-7	breast:	n/a	n/a
39	ZNF263	chr19:44059278-44059883	HEK293-T-REx	kidney:	n/a	chr19:44059717-44059726
40	RAD21	chr19:44059256-44059856	HCT-116	colon:	n/a	n/a
41	BHLHE40	chr19:44059354-44059660	K562	blood:	n/a	n/a
42	RAD21	chr19:44059332-44059732	IMR90	lung:	n/a	n/a
43	CTCF	chr19:44059295-44059736	K562	blood:	n/a	n/a
44	CTCF	chr19:44059292-44059714	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr19:44059398-44059746	ECC-1	luminal epithelium:	n/a	n/a
46	RAD21	chr19:44059276-44059771	A549	lung:	n/a	n/a
47	CTCF	chr19:44059217-44059817	HCT-116	colon:	n/a	n/a
48	CTCF	chr19:44059360-44059676	GM12878	blood:	n/a	n/a
49	CTCF	chr19:44059377-44059664	A549	lung:	n/a	n/a
50	CTCF	chr19:44059359-44059641	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44059054..44060074-chr19:44156198..44156967,3	K562	blood:
2	chr19:44059108..44059674-chr19:44098601..44099306,2	MCF-7	breast:
3	chr19:43937158..43937719-chr19:44059063..44059904,2	K562	blood:
4	chr19:44058980..44059977-chr19:44099035..44099807,2	MCF-7	breast:
5	chr19:44059035..44059991-chr19:44156189..44157100,4	MCF-7	breast:
6	chr19:44058393..44061505-chr19:44095706..44100146,4	MCF-7	breast:
7	chr19:44059273..44059814-chr19:44100326..44101062,2	MCF-7	breast:
8	chr19:44059185..44060976-chr19:44078373..44080974,2	K562	blood:
9	chr19:44059581..44061634-chr19:44072814..44074549,2	MCF-7	breast:

No data

Variant related genes	Relation type
XRCC1	TF binding region
ENSG00000124444	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000269583	Chromatin interaction
ENSG00000268361	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs168310	1.00[ASN][1000 genomes]
rs2854497	1.00[ASN][1000 genomes]
rs3213316	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213321	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213322	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	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60273962	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60889018	1.00[ASN][1000 genomes]
rs7257640	1.00[ASN][1000 genomes]
rs73554667	1.00[ASN][1000 genomes]
rs73554679	1.00[ASN][1000 genomes]
rs73554696	1.00[ASN][1000 genomes]
rs73556565	1.00[ASN][1000 genomes]
rs73556581	1.00[ASN][1000 genomes]
rs8104645	1.00[ASN][1000 genomes]
rs8110767	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	chr19:44040800-44060800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:44041800-44065200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:44043200-44064600	Weak transcription	NHDF-Ad	bronchial
5	chr19:44043600-44065800	Strong transcription	Adipose Nuclei	Adipose
6	chr19:44043800-44065800	Weak transcription	Fetal Heart	heart
7	chr19:44043800-44074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:44044600-44069000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:44045200-44062800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:44047400-44066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:44048200-44062000	Weak transcription	NH-A	brain
12	chr19:44048200-44067000	Weak transcription	HUVEC	blood vessel
13	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
14	chr19:44050400-44063000	Strong transcription	Thymus	Thymus
15	chr19:44052600-44060600	Strong transcription	Osteobl	bone
16	chr19:44052800-44060400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:44052800-44068400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:44053000-44060000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:44053000-44064800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:44053000-44065600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:44053000-44066200	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:44053200-44064600	Weak transcription	K562	blood
23	chr19:44053400-44061000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:44053400-44068800	Strong transcription	Fetal Intestine Small	intestine
25	chr19:44053400-44069400	Strong transcription	Fetal Stomach	stomach
26	chr19:44053600-44062400	Strong transcription	Dnd41	blood
27	chr19:44053600-44068600	Strong transcription	Fetal Intestine Large	intestine
28	chr19:44053800-44060600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:44053800-44060600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:44053800-44062600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:44054000-44060000	Strong transcription	Brain Germinal Matrix	brain
32	chr19:44054000-44065600	Strong transcription	Placenta	Placenta
33	chr19:44054200-44060200	Strong transcription	Colon Smooth Muscle	Colon
34	chr19:44054200-44061200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:44054400-44060000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr19:44054400-44060200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:44054400-44060400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:44054400-44062400	Strong transcription	Primary T cells from cord blood	blood
39	chr19:44054400-44062400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:44054600-44061200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr19:44054600-44062400	Strong transcription	HSMM	muscle
42	chr19:44055200-44061000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:44056000-44066600	Weak transcription	Psoas Muscle	Psoas
44	chr19:44056400-44064600	Weak transcription	Aorta	Aorta
45	chr19:44056400-44064800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:44056400-44066400	Weak transcription	Stomach Mucosa	stomach
47	chr19:44057200-44060400	Strong transcription	Fetal Kidney	kidney
48	chr19:44057200-44067000	Weak transcription	Fetal Brain Male	brain
49	chr19:44057400-44060800	Strong transcription	GM12878-XiMat	blood
50	chr19:44057600-44061800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links