Variant report

Variant	rs28900976
Chromosome Location	chr2:234740481-234740482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234614862..234617067-chr2:234739874..234742811,2	MCF-7	breast:
2	chr2:234404504..234406876-chr2:234739242..234740869,2	MCF-7	breast:
3	chr2:234607784..234610773-chr2:234739083..234742311,4	MCF-7	breast:
4	chr2:234160919..234163001-chr2:234739570..234741620,2	MCF-7	breast:
5	chr2:234738464..234743191-chr2:234754553..234759702,7	K562	blood:
6	chr2:234388065..234390771-chr2:234740107..234742680,2	MCF-7	breast:
7	chr2:234599519..234601666-chr2:234740030..234742555,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs28626554	0.83[CHB][hapmap]
rs28899475	1.00[AMR][1000 genomes]
rs28900418	1.00[AMR][1000 genomes]
rs28900677	0.83[CHB][hapmap]
rs28900694	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs28900695	0.84[ASN][1000 genomes]
rs28900714	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28900716	1.00[AMR][1000 genomes]
rs28900723	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs28900724	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs28901606	1.00[JPT][hapmap]
rs28901612	1.00[JPT][hapmap]
rs28901616	0.88[JPT][hapmap]
rs28901617	0.88[JPT][hapmap]
rs28901623	1.00[JPT][hapmap]
rs28946894	1.00[AMR][1000 genomes]
rs35542629	1.00[AMR][1000 genomes]
rs3771333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59046407	1.00[AMR][1000 genomes]
rs61200559	1.00[AMR][1000 genomes]
rs73120730	1.00[AMR][1000 genomes]
rs73120736	1.00[AMR][1000 genomes]
rs73120743	1.00[AMR][1000 genomes]
rs7591879	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876020	chr2:234724225-234748814	Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv470523	chr2:234725819-234740490	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv876021	chr2:234725819-234748814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv876022	chr2:234726154-234748814	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv984453	chr2:234726749-234740629	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1008316	chr2:234728911-234758539	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234731800-234741200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:234732000-234741200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:234732200-234742000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:234733400-234742200	Weak transcription	Liver	Liver
5	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
6	chr2:234737800-234741600	Weak transcription	Dnd41	blood
7	chr2:234738200-234741000	Weak transcription	Osteobl	bone
8	chr2:234738200-234744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
10	chr2:234738400-234741600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:234738400-234741800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:234738800-234743000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:234738800-234744000	Weak transcription	NHLF	lung
14	chr2:234739000-234740800	Strong transcription	Fetal Stomach	stomach
15	chr2:234739000-234742600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:234739000-234742600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:234739200-234742600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:234739200-234743000	Weak transcription	HepG2	liver
19	chr2:234739400-234741000	Genic enhancers	A549	lung
20	chr2:234739400-234742600	Enhancers	Fetal Muscle Trunk	muscle
21	chr2:234739400-234744000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:234739600-234747600	Weak transcription	Brain Germinal Matrix	brain
23	chr2:234739800-234742600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:234739800-234752800	Weak transcription	Spleen	Spleen
25	chr2:234740000-234741400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:234740000-234742400	Weak transcription	Fetal Thymus	thymus
27	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
28	chr2:234740200-234740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:234740200-234741000	Weak transcription	NHEK	skin
30	chr2:234740200-234741400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:234740200-234741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:234740200-234741600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:234740200-234742600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:234740200-234742800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:234740200-234743000	Weak transcription	HMEC	breast
36	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
37	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood

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