Variant report

Variant	rs3856719
Chromosome Location	chr3:112996541-112996542
allele	A/C/G/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	EP300	chr3:112996309-112996593	GM12878	blood:	n/a	n/a
2	SPI1	chr3:112996256-112996596	GM12891	blood:	n/a	chr3:112996564-112996577
3	BHLHE40	chr3:112996457-112996636	GM12878	blood:	n/a	n/a
4	SPI1	chr3:112996346-112996577	GM12878	blood:	n/a	chr3:112996564-112996577
5	MEF2A	chr3:112996106-112996726	GM12878	blood:	n/a	n/a
6	EP300	chr3:112996396-112996608	GM12878	blood:	n/a	n/a
7	MAZ	chr3:112996234-112996568	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr3:112996451-112996580	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112995543..112998104-chr3:113010327..113013877,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region
ENSG00000206530	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10511323	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710894	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717833	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919134	0.90[AMR][1000 genomes]
rs11928342	0.82[AMR][1000 genomes]
rs12485329	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492273	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12494864	0.89[EUR][1000 genomes]
rs12631733	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638030	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16860758	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860787	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860792	0.86[AMR][1000 genomes]
rs2036282	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34284771	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814398	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846046	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856718	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856720	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271357	0.92[AMR][1000 genomes]
rs4682131	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682132	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682478	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682479	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682481	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682483	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235143	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73235147	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7641410	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs775222	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
2	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
6	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:112990600-113004000	Weak transcription	NHEK	skin
9	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
13	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
15	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:112994800-112997400	Weak transcription	Gastric	stomach
17	chr3:112995200-112996800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:112995200-112997000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:112995200-112997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:112995200-112999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:112995200-113001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:112995400-112996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:112995400-112996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:112995400-112996800	Weak transcription	Esophagus	oesophagus
27	chr3:112995400-112997000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:112995400-112997000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:112995400-112997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:112995400-112997000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:112995400-112998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
35	chr3:112995400-113035800	Weak transcription	Lung	lung
36	chr3:112995600-112996800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:112995600-112996800	Enhancers	Primary B cells from cord blood	blood
38	chr3:112995600-112997000	Weak transcription	Fetal Brain Female	brain
39	chr3:112995600-112997200	Enhancers	Spleen	Spleen
40	chr3:112995600-112998200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:112995800-112996600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:112995800-112996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:112995800-112997000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:112995800-112997000	Genic enhancers	Fetal Muscle Leg	muscle
47	chr3:112995800-112997000	Weak transcription	Ovary	ovary
48	chr3:112995800-112997200	Enhancers	Brain Substantia Nigra	brain
49	chr3:112995800-112997400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:112995800-112997400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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