Variant report

Variant	rs12130044
Chromosome Location	chr1:93457838-93457839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93426802..93428394-chr1:93457391..93459603,2	K562	blood:
2	chr1:93317754..93320397-chr1:93457580..93459543,2	K562	blood:
3	chr1:93304783..93306730-chr1:93457486..93459608,2	K562	blood:

Variant related genes	Relation type
ENSG00000207523	Chromatin interaction
ENSG00000154511	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1011663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10747454	0.88[ASN][1000 genomes]
rs11164850	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164851	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049007	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120036	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133990	0.85[ASN][1000 genomes]
rs12144226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678784	0.93[ASN][1000 genomes]
rs2086314	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127398	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127400	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561471	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3943283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515797	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847226	0.99[ASN][1000 genomes]
rs4847389	0.84[ASN][1000 genomes]
rs514235	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs521428	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs534409	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs567613	0.88[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs594527	0.93[ASN][1000 genomes]
rs606344	0.93[ASN][1000 genomes]
rs619784	0.93[ASN][1000 genomes]
rs641462	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs660870	0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs663112	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671268	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs6681429	0.81[ASN][1000 genomes]
rs7517539	0.94[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7524934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753391	0.92[ASN][1000 genomes]
rs770883	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs945630	0.83[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12130044	FAM69A	Cis_1M	lymphoblastoid	RTeQTL
rs12130044	FAM69A	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93451800-93466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:93452400-93458600	Weak transcription	HSMMtube	muscle
3	chr1:93454400-93458800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:93454600-93458000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:93454600-93458200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:93454600-93458400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:93454600-93458800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:93454600-93459800	Enhancers	Primary T cells from cord blood	blood
9	chr1:93454600-93459800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:93454800-93458200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:93454800-93459800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:93455400-93459800	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:93456000-93461000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:93456200-93461200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:93456400-93459800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:93456600-93459600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:93456600-93459800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:93456600-93459800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:93456600-93459800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:93457200-93458000	Flanking Active TSS	Dnd41	blood
21	chr1:93457400-93458200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:93457400-93458200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:93457400-93459000	Weak transcription	Thymus	Thymus
24	chr1:93457400-93459200	Weak transcription	HepG2	liver
25	chr1:93457600-93458000	Enhancers	HSMM	muscle
26	chr1:93457600-93458000	Enhancers	NHDF-Ad	bronchial
27	chr1:93457800-93459200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:93457800-93459200	Weak transcription	K562	blood

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