Variant report

Variant	rs28376014
Chromosome Location	chr4:3309029-3309030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3309013-3309063	AG04450	lung:	fetal
2	chr4:3309013-3309063	HL-60	blood:	n/a
3	chr4:3309013-3309063	HMEC	breast:	n/a
4	chr4:3309013-3309063	H1-hESC	embryonic stem cell:	embryo
5	chr4:3309013-3309063	HEK293	kidney:	embryo
6	chr4:3309013-3309063	NH-A	brain:	n/a
7	chr4:3309013-3309063	NHBE	bronchial:	n/a
8	chr4:3309013-3309063	HCM	heart:	n/a
9	chr4:3309013-3309063	HRPEpiC	eye:	n/a
10	chr4:3309013-3309063	NHDF-neo	bronchial:	n/a
11	chr4:3309013-3309063	AG09319	gingival:	n/a
12	chr4:3309013-3309063	CMK	blood:	n/a
13	chr4:3309013-3309063	NB4	blood:	n/a
14	chr4:3309013-3309063	SK-N-SH	brain:	n/a
15	chr4:3309013-3309063	HNPCEpiC	eye:	n/a
16	chr4:3309013-3309063	GM12878	blood:	n/a
17	chr4:3309013-3309063	Jurkat	blood:	n/a
18	chr4:3309013-3309063	HUVEC	blood vessel:	n/a
19	chr4:3309013-3309063	HCF	heart:	n/a
20	chr4:3309013-3309063	HPAEpiC	pulmonary alveolar:	n/a
21	chr4:3309013-3309063	PrEC	prostate:	n/a
22	chr4:3309013-3309063	GM12892	blood:	n/a
23	chr4:3309013-3309063	PFSK-1	brain:	n/a
24	chr4:3309013-3309063	BJ	skin:	n/a
25	chr4:3309013-3309063	IMR90	lung:	fetal
26	chr4:3309013-3309063	GM12891	blood:	n/a
27	chr4:3309013-3309063	BE2_C	brain:	n/a
28	chr4:3309013-3309063	AG04449	skin:	fetal
29	chr4:3309013-3309063	MCF10A-Er-Src	breast:	n/a
30	chr4:3309013-3309063	HRE	kidney:	n/a
31	chr4:3309013-3309063	HRCEpiC	kidney:	n/a
32	chr4:3309013-3309063	A549	lung:	n/a
33	chr4:3309013-3309063	HEEpiC	esophagus:	n/a
34	chr4:3309013-3309063	Hepatocyte	liver:	n/a
35	chr4:3309013-3309063	LNCaP	prostate:	n/a
36	chr4:3309013-3309063	NT2-D1	testis:	n/a
37	chr4:3309013-3309063	HCT-116	colon:	n/a
38	chr4:3309013-3309063	SK-N-SH_RA	brain:	n/a
39	chr4:3309013-3309063	AoSMC	blood vessel:	n/a
40	chr4:3309013-3309063	AG09309	skin:	n/a
41	chr4:3309013-3309063	MCF-7	breast:	n/a
42	chr4:3309013-3309063	RPTEC	kidney:	n/a
43	chr4:3309013-3309063	GM06990	blood:	n/a
44	chr4:3309013-3309063	SAEC	small airway:	n/a
45	chr4:3309013-3309063	GM19239	blood:	n/a
46	chr4:3309013-3309063	AG10803	skin:	n/a
47	chr4:3309013-3309063	HIPEpiC	eye:	n/a
48	chr4:3309013-3309063	ovcar-3	ovarian:	n/a
49	chr4:3309013-3309063	HCPEpiC	choroid plexus:	n/a
50	chr4:3309013-3309063	K562	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr4:3297413..3300399-chr4:3305342..3309576,4	MCF-7	breast:
2	chr4:3307561..3309945-chr4:3316347..3319248,2	MCF-7	breast:
3	chr4:3293251..3296512-chr4:3305842..3309963,7	MCF-7	breast:

No data

Variant related genes	Relation type
RGS12	CpG island
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10011241	0.85[AMR][1000 genomes]
rs28728173	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3025799	0.85[AMR][1000 genomes]
rs9995687	1.00[AMR][1000 genomes];1.00[EUR][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers 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 target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
12	nsv966506	chr4:3308550-3320391	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:3299200-3310000	Enhancers	HUVEC	blood vessel
3	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
4	chr4:3301000-3310400	Enhancers	Fetal Muscle Leg	muscle
5	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:3301600-3312400	Enhancers	Fetal Muscle Trunk	muscle
7	chr4:3303200-3310800	Enhancers	Fetal Brain Male	brain
8	chr4:3303600-3310600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:3304000-3313000	Weak transcription	HepG2	liver
10	chr4:3304200-3310600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:3304400-3309800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:3304400-3310600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:3304800-3318600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:3305000-3309200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:3306000-3309800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:3306000-3310400	Enhancers	Spleen	Spleen
17	chr4:3306600-3309800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:3306600-3312600	Enhancers	Lung	lung
19	chr4:3306600-3320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:3306800-3312400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr4:3306800-3312800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:3307000-3309800	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:3307000-3310600	Enhancers	Brain Germinal Matrix	brain
24	chr4:3307000-3310600	Enhancers	Fetal Brain Female	brain
25	chr4:3307000-3320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:3307200-3309200	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:3307200-3318000	Weak transcription	Liver	Liver
28	chr4:3307200-3327000	Weak transcription	Fetal Kidney	kidney
29	chr4:3307400-3312200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:3307400-3325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:3307400-3326800	Weak transcription	A549	lung
32	chr4:3307600-3309400	Enhancers	Fetal Thymus	thymus
33	chr4:3307600-3315000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:3307600-3322200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:3307600-3323000	Weak transcription	NH-A	brain
36	chr4:3307600-3323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:3307800-3311600	Weak transcription	Fetal Intestine Large	intestine
38	chr4:3307800-3312200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:3307800-3319000	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:3308000-3309600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:3308000-3310400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:3308000-3311600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:3308000-3313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:3308000-3318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:3308000-3318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:3308000-3319800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:3308000-3322800	Weak transcription	NHDF-Ad	bronchial
48	chr4:3308000-3323600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:3308000-3323800	Weak transcription	Osteobl	bone
50	chr4:3308000-3326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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