Variant report

Variant	rs2625282
Chromosome Location	chr3:101484335-101484336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101482859..101484474-chr3:101486129..101487850,2	K562	blood:
2	chr3:101484277..101486905-chr3:101489538..101492102,2	MCF-7	breast:
3	chr3:101480738..101484474-chr3:101485268..101487879,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13090844	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2449492	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2449493	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2466369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611840	1.00[ASN][1000 genomes]
rs2625283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2625289	0.96[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2722162	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2722166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605621	0.81[EUR][1000 genomes]
rs665631	1.00[MEX][hapmap]
rs6764700	0.93[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs6794860	1.00[ASW][hapmap];0.93[TSI][hapmap]
rs6805496	0.92[TSI][hapmap]
rs6806256	0.93[TSI][hapmap]

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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv963500	chr3:101481412-101496033	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2625282	FAM55C	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:101464200-101486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:101472800-101488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:101473000-101484400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:101473000-101485400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:101473000-101485400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:101473000-101486000	Strong transcription	Dnd41	blood
9	chr3:101473400-101484600	Strong transcription	Fetal Thymus	thymus
10	chr3:101473800-101484600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:101473800-101487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:101474000-101484400	Strong transcription	Thymus	Thymus
13	chr3:101474200-101484400	Strong transcription	Primary T cells from cord blood	blood
14	chr3:101474200-101484400	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:101474400-101485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:101474800-101490600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:101475000-101486400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:101475600-101485800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:101475600-101488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:101477000-101487200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:101477200-101497400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:101477400-101486400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:101477400-101486600	Weak transcription	Esophagus	oesophagus
24	chr3:101477400-101497600	Weak transcription	Right Ventricle	heart
25	chr3:101477600-101486000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:101477600-101486000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:101477600-101488400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:101477600-101488400	Weak transcription	Spleen	Spleen
29	chr3:101477600-101497400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:101477800-101487800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:101478000-101489000	Weak transcription	Gastric	stomach
32	chr3:101478000-101497400	Weak transcription	NHEK	skin
33	chr3:101478400-101485600	Weak transcription	Psoas Muscle	Psoas
34	chr3:101478400-101487000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:101478600-101486200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:101478600-101487000	Weak transcription	HepG2	liver
37	chr3:101478600-101488000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:101478600-101488400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:101478600-101489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:101478600-101497400	Weak transcription	A549	lung
41	chr3:101478600-101497400	Weak transcription	K562	blood
42	chr3:101478800-101488200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:101478800-101490400	Weak transcription	Ovary	ovary
44	chr3:101479000-101486200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:101479000-101487200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:101479000-101488400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:101479000-101497400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:101479200-101490000	Weak transcription	Fetal Kidney	kidney
49	chr3:101479200-101497400	Weak transcription	NHLF	lung
50	chr3:101480200-101484400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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