Variant report

Variant	rs73859925
Chromosome Location	chr3:99833335-99833336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:99833309-99833361	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr3:99833257-99833989	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:99833278-99833405	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:99833246-99833376	A549	lung:	n/a	n/a
5	POLR2A	chr3:99833332-99833337	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:99833293-99833343	AG04449	skin:	fetal
2	chr3:99833293-99833343	T-47D	breast:	n/a
3	chr3:99833293-99833343	NH-A	brain:	n/a
4	chr3:99833293-99833343	NT2-D1	testis:	n/a
5	chr3:99833293-99833343	GM19239	blood:	n/a
6	chr3:99833293-99833343	HEEpiC	esophagus:	n/a
7	chr3:99833293-99833343	SK-N-SH_RA	brain:	n/a
8	chr3:99833293-99833343	BE2_C	brain:	n/a
9	chr3:99833293-99833343	HUVEC	blood vessel:	n/a
10	chr3:99833293-99833343	SAEC	small airway:	n/a
11	chr3:99833293-99833343	Jurkat	blood:	n/a
12	chr3:99833293-99833343	SKMC	muscle:	n/a
13	chr3:99833293-99833343	NHBE	bronchial:	n/a
14	chr3:99833293-99833343	HCM	heart:	n/a
15	chr3:99833293-99833343	HCT-116	colon:	n/a
16	chr3:99833293-99833343	GM12878	blood:	n/a
17	chr3:99833293-99833343	SK-N-MC	brain:	n/a
18	chr3:99833293-99833343	LNCaP	prostate:	n/a
19	chr3:99833293-99833343	AG09309	skin:	n/a
20	chr3:99833293-99833343	HMEC	breast:	n/a
21	chr3:99833293-99833343	U87	brain:	n/a
22	chr3:99833293-99833343	ECC-1	luminal epithelium:	n/a
23	chr3:99833293-99833343	IMR90	lung:	fetal
24	chr3:99833293-99833343	HNPCEpiC	eye:	n/a
25	chr3:99833293-99833343	GM12892	blood:	n/a
26	chr3:99833293-99833343	H1-hESC	embryonic stem cell:	embryo
27	chr3:99833293-99833343	HCF	heart:	n/a
28	chr3:99833293-99833343	Caco-2	colon:	n/a
29	chr3:99833293-99833343	HEK293	kidney:	embryo
30	chr3:99833293-99833343	AG04450	lung:	fetal
31	chr3:99833293-99833343	AoSMC	blood vessel:	n/a
32	chr3:99833293-99833343	SK-N-SH	brain:	n/a
33	chr3:99833293-99833343	PANC-1	pancreas:	n/a
34	chr3:99833293-99833343	HIPEpiC	eye:	n/a
35	chr3:99833293-99833343	HL-60	blood:	n/a
36	chr3:99833293-99833343	NB4	blood:	n/a
37	chr3:99833293-99833343	ProgFib	skin:	n/a
38	chr3:99833293-99833343	Hepatocyte	liver:	n/a
39	chr3:99833293-99833343	AG09319	gingival:	n/a
40	chr3:99833293-99833343	MCF10A-Er-Src	breast:	n/a
41	chr3:99833293-99833343	HAEpiC	amniotic membrane:	n/a
42	chr3:99833293-99833343	MCF-7	breast:	n/a
43	chr3:99833293-99833343	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:99833293-99833343	HRCEpiC	kidney:	n/a
45	chr3:99833293-99833343	HRE	kidney:	n/a
46	chr3:99833293-99833343	A549	lung:	n/a
47	chr3:99833293-99833343	CMK	blood:	n/a
48	chr3:99833293-99833343	GM12891	blood:	n/a
49	chr3:99833293-99833343	HCPEpiC	choroid plexus:	n/a
50	chr3:99833293-99833343	AG10803	skin:	n/a

No data

Variant related genes	Relation type
CMSS1	TF binding region
FILIP1L	TF binding region
CMSS1	CpG island
FILIP1L	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs403858	0.93[AFR][1000 genomes]
rs55721822	0.93[AFR][1000 genomes]
rs55978866	0.80[AFR][1000 genomes]
rs56186146	0.93[AFR][1000 genomes]
rs56227134	1.00[AFR][1000 genomes]
rs56678433	0.89[AFR][1000 genomes]
rs58953554	0.93[AFR][1000 genomes]
rs6783067	0.85[AFR][1000 genomes]
rs73858965	0.82[AFR][1000 genomes]
rs73858967	0.82[AFR][1000 genomes]
rs73859912	0.82[AFR][1000 genomes]
rs73859914	0.82[AFR][1000 genomes]
rs73859915	0.82[AFR][1000 genomes]
rs73859916	0.82[AFR][1000 genomes]
rs73859919	0.82[AFR][1000 genomes]
rs73859924	1.00[AFR][1000 genomes]
rs73859931	0.93[AFR][1000 genomes]
rs7640817	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99818000-99836600	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99823600-99837200	Weak transcription	Pancreas	Pancrea
4	chr3:99825200-99835000	Weak transcription	K562	blood
5	chr3:99825200-99840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:99825200-99844000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:99825200-99844200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:99825600-99841000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:99826200-99838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:99827400-99839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:99827800-99834200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr3:99829200-99841000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:99829400-99833400	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:99830000-99841200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:99831400-99833600	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:99831400-99841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:99832200-99833800	Enhancers	Psoas Muscle	Psoas
19	chr3:99832400-99833800	Enhancers	NHEK	skin
20	chr3:99832600-99833800	Enhancers	Right Ventricle	heart
21	chr3:99832600-99835800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:99832800-99833400	Enhancers	Esophagus	oesophagus
23	chr3:99832800-99833600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:99832800-99833600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:99833000-99833400	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr3:99833000-99833800	Enhancers	Placenta	Placenta
27	chr3:99833000-99833800	Enhancers	Stomach Smooth Muscle	stomach
28	chr3:99833000-99835200	Enhancers	HepG2	liver
29	chr3:99833200-99833400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:99833200-99833400	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr3:99833200-99833400	Flanking Active TSS	Left Ventricle	heart
32	chr3:99833200-99833400	Flanking Active TSS	Right Atrium	heart
33	chr3:99833200-99833800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:99833200-99833800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:99833200-99833800	ZNF genes & repeats	Aorta	Aorta
36	chr3:99833200-99833800	Enhancers	Ovary	ovary
37	chr3:99833200-99834200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:99833200-99839600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links