Variant report

Variant	rs1060737
Chromosome Location	chr2:30864789-30864790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30859615..30861483-chr2:30862535..30865064,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11127281	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11692096	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11895131	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs11901266	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1252627	0.85[CHB][hapmap]
rs1252632	0.81[ASN][1000 genomes]
rs1252633	0.81[ASN][1000 genomes]
rs1252635	1.00[CHB][hapmap]
rs1286	0.87[ASN][1000 genomes]
rs17395007	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17395091	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1807334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869422	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2244911	0.80[ASN][1000 genomes]
rs2250956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253299	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2262947	0.90[ASN][1000 genomes]
rs2593436	0.89[ASN][1000 genomes]
rs2593445	0.82[CHB][hapmap]
rs2593446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593454	0.83[EUR][1000 genomes]
rs2593473	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2602781	0.84[ASN][1000 genomes]
rs2602795	0.89[ASN][1000 genomes]
rs2602796	0.90[ASN][1000 genomes]
rs2602803	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2602809	0.87[ASN][1000 genomes]
rs2609919	0.90[ASN][1000 genomes]
rs2609920	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2609944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609957	0.86[ASN][1000 genomes]
rs2609961	0.81[ASN][1000 genomes]
rs711241	1.00[CHB][hapmap]
rs7559747	0.80[ASN][1000 genomes]
rs829566	1.00[CHB][hapmap]
rs829568	1.00[CHB][hapmap]
rs829621	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs829624	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs829625	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs829640	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs829643	1.00[CHB][hapmap]
rs829652	1.00[CHB][hapmap]
rs829674	1.00[CHB][hapmap]
rs829676	1.00[CHB][hapmap]
rs829683	1.00[CHB][hapmap]
rs829685	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
2	nsv581266	chr2:30864789-30874229	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1060737	SLC4A1AP	cis	cerebellum	SCAN
rs1060737	ALK	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30835800-30871200	Weak transcription	Small Intestine	intestine
2	chr2:30841800-30872200	Weak transcription	Spleen	Spleen
3	chr2:30843400-30864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:30845600-30877800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:30845800-30877800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:30850200-30874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:30850400-30865000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:30850400-30869200	Weak transcription	Gastric	stomach
9	chr2:30850400-30874600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:30851400-30865000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:30851800-30865000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:30853200-30867200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:30853200-30872000	Weak transcription	NHDF-Ad	bronchial
14	chr2:30854000-30867000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:30854200-30867600	Weak transcription	Psoas Muscle	Psoas
16	chr2:30854400-30865000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:30854400-30865200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:30854400-30866600	Weak transcription	GM12878-XiMat	blood
19	chr2:30854600-30864800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:30855000-30865000	Weak transcription	Fetal Intestine Small	intestine
21	chr2:30855000-30865400	Weak transcription	HSMM	muscle
22	chr2:30855600-30867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:30856400-30866600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:30857000-30869000	Weak transcription	Hela-S3	cervix
25	chr2:30858600-30865400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:30859600-30872000	Weak transcription	Fetal Stomach	stomach
27	chr2:30860200-30865000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:30860200-30866200	Weak transcription	HUVEC	blood vessel
29	chr2:30860400-30878200	Weak transcription	NHLF	lung
30	chr2:30861400-30876800	Weak transcription	Fetal Heart	heart
31	chr2:30861600-30864800	Strong transcription	Primary B cells from cord blood	blood
32	chr2:30861600-30864800	Weak transcription	NHEK	skin
33	chr2:30861600-30865200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:30861600-30872200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:30862000-30868600	Weak transcription	Brain Substantia Nigra	brain
36	chr2:30862200-30865200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:30862400-30864800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:30862400-30866800	Weak transcription	HMEC	breast
39	chr2:30862400-30868400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:30862600-30865000	Weak transcription	Fetal Kidney	kidney
41	chr2:30862600-30865200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:30862800-30865200	Strong transcription	Dnd41	blood
43	chr2:30862800-30865600	Strong transcription	Fetal Lung	lung
44	chr2:30863000-30864800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:30863000-30865200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:30863000-30865200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:30863000-30865200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:30863000-30865200	Strong transcription	A549	lung
49	chr2:30863000-30865400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:30863000-30866000	Weak transcription	Adipose Nuclei	Adipose

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