Variant report

Variant	rs4669402
Chromosome Location	chr2:9779413-9779414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9774003..9777519-chr2:9779253..9781345,3	MCF-7	breast:
2	chr2:9767473..9774138-chr2:9774735..9780659,16	MCF-7	breast:
3	chr2:9769155..9773590-chr2:9774278..9779571,11	MCF-7	breast:
4	chr2:9779400..9780949-chr2:9782818..9785036,2	K562	blood:

Variant related genes	Relation type
ENSG00000134308	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10427360	0.97[ASN][1000 genomes]
rs10495569	0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12620485	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806668	0.89[ASN][1000 genomes]
rs1976902	0.85[CHB][hapmap]
rs2091210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3762535	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4145375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668626	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4669403	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4669404	0.82[ASN][1000 genomes]
rs56068986	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432026	0.99[ASN][1000 genomes]
rs6432027	0.92[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6715748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732745	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs73913149	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73913150	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73913152	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7567578	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884427	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1011802	chr2:9766171-9808284	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3401275	chr2:9775301-9779799	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
4	nsv518363	chr2:9777229-9788315	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9772200-9781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:9772800-9780200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:9775000-9782800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:9776400-9779600	Enhancers	Brain Substantia Nigra	brain
5	chr2:9776400-9782000	Enhancers	HMEC	breast
6	chr2:9776600-9780200	Enhancers	HSMM	muscle
7	chr2:9776600-9781200	Enhancers	NHDF-Ad	bronchial
8	chr2:9776800-9779800	Enhancers	Osteobl	bone
9	chr2:9776800-9780000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:9776800-9780600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:9776800-9780600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:9776800-9781000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:9777000-9779600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:9777000-9779800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:9777000-9779800	Enhancers	NH-A	brain
16	chr2:9777000-9780000	Enhancers	HSMMtube	muscle
17	chr2:9777000-9781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:9777000-9781000	Enhancers	K562	blood
19	chr2:9777200-9779800	Enhancers	Fetal Muscle Leg	muscle
20	chr2:9777200-9781000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:9777200-9781000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:9777400-9780800	Enhancers	Fetal Heart	heart
23	chr2:9777400-9781000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:9777600-9779600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:9777600-9779600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:9777600-9779600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:9777600-9779600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:9777600-9779600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:9777600-9779800	Enhancers	Hela-S3	cervix
30	chr2:9777600-9780200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:9777600-9780200	Enhancers	Fetal Muscle Trunk	muscle
32	chr2:9777600-9781000	Enhancers	Ovary	ovary
33	chr2:9777800-9779800	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:9777800-9780200	Enhancers	Lung	lung
35	chr2:9777800-9780400	Enhancers	Placenta	Placenta
36	chr2:9777800-9780400	Enhancers	Fetal Stomach	stomach
37	chr2:9777800-9781000	Enhancers	Left Ventricle	heart
38	chr2:9778000-9779800	Enhancers	Adipose Nuclei	Adipose
39	chr2:9778000-9779800	Enhancers	Colon Smooth Muscle	Colon
40	chr2:9778000-9780200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:9778000-9780200	Enhancers	Right Atrium	heart
42	chr2:9778200-9780200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:9778400-9779600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:9778400-9779600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:9778400-9779800	Enhancers	Fetal Kidney	kidney
46	chr2:9778600-9780200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:9778600-9782800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:9778800-9779600	Weak transcription	Fetal Intestine Small	intestine
49	chr2:9778800-9779800	Weak transcription	Liver	Liver
50	chr2:9778800-9780000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links