Variant report

Variant	rs7580131
Chromosome Location	chr2:33546609-33546610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33546250..33548887-chr2:33557480..33559960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252246	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10189109	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191688	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1058840	0.94[ASW][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs11684935	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1453842	0.84[CHD][hapmap]
rs2276591	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4569454	0.85[CHB][hapmap]
rs6737863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs723042	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33523800-33550600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:33529800-33561000	Weak transcription	HUVEC	blood vessel
4	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
5	chr2:33540800-33580800	Weak transcription	Placenta	Placenta
6	chr2:33541000-33547000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:33541200-33547200	Weak transcription	Gastric	stomach
8	chr2:33542000-33572200	Weak transcription	Liver	Liver
9	chr2:33543000-33547000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:33543000-33547200	Weak transcription	Lung	lung
11	chr2:33544600-33547400	Enhancers	Ovary	ovary
12	chr2:33544800-33547200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:33544800-33548400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:33545000-33547200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:33545000-33547600	Enhancers	Fetal Heart	heart
16	chr2:33545200-33546800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:33545200-33549600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:33545400-33547800	Enhancers	Adipose Nuclei	Adipose
19	chr2:33545400-33548400	Enhancers	Fetal Stomach	stomach
20	chr2:33545400-33551800	Weak transcription	Right Atrium	heart
21	chr2:33545600-33547600	Enhancers	Fetal Muscle Leg	muscle
22	chr2:33545600-33547800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:33545600-33547800	Enhancers	HSMMtube	muscle
24	chr2:33545600-33548200	Enhancers	NHLF	lung
25	chr2:33545800-33547800	Enhancers	Fetal Lung	lung
26	chr2:33545800-33548200	Enhancers	Colon Smooth Muscle	Colon
27	chr2:33545800-33548200	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:33545800-33548400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:33545800-33549200	Enhancers	Dnd41	blood
30	chr2:33546000-33546800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:33546200-33547200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:33546200-33547200	Enhancers	HMEC	breast
33	chr2:33546200-33547200	Enhancers	NH-A	brain
34	chr2:33546200-33548400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:33546400-33546800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:33546400-33546800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:33546400-33546800	Enhancers	A549	lung
38	chr2:33546400-33546800	Flanking Active TSS	GM12878-XiMat	blood
39	chr2:33546400-33547000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:33546400-33547200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:33546400-33547400	Enhancers	Aorta	Aorta
42	chr2:33546400-33547400	Flanking Active TSS	Osteobl	bone
43	chr2:33546400-33547600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:33546400-33547800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:33546400-33547800	Enhancers	HSMM	muscle
46	chr2:33546600-33546800	Enhancers	Left Ventricle	heart
47	chr2:33546600-33546800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:33546600-33546800	Enhancers	Spleen	Spleen
49	chr2:33546600-33546800	Active TSS	NHDF-Ad	bronchial
50	chr2:33546600-33547000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links