Variant report

Variant	rs10875749
Chromosome Location	chr12:48531917-48531918
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48530838..48532658-chr12:48534908..48536474,2	K562	blood:
2	chr12:48530838..48533486-chr12:48533641..48536474,3	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161358	0.85[EUR][1000 genomes]
rs10875716	0.81[CEU][hapmap]
rs10875718	0.80[CEU][hapmap]
rs10875719	0.80[CEU][hapmap]
rs10875743	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10875753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap]
rs11168351	0.81[CEU][hapmap]
rs11168352	0.80[YRI][hapmap]
rs11168408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168437	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12099462	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12228750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12816820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs3997	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4760679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	0.92[CEU][hapmap]
rs6580652	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580654	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295580	0.82[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap]
rs7486941	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7487682	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7971880	0.81[CEU][hapmap]
rs7975632	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973398	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9971924	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv558790	chr12:48529168-48539888	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10875749	H1FNT	cis	Muscle Skeletal	GTEx
rs10875749	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
12	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
17	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
19	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
26	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
27	chr12:48522400-48534400	Weak transcription	NHDF-Ad	bronchial
28	chr12:48522600-48532800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:48523400-48546600	Strong transcription	Fetal Muscle Leg	muscle
30	chr12:48523800-48540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:48524000-48536400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:48525000-48536400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:48525000-48539800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:48525400-48536600	Weak transcription	Right Atrium	heart
36	chr12:48525600-48546200	Strong transcription	A549	lung
37	chr12:48525800-48535600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:48526200-48547600	Strong transcription	Adipose Nuclei	Adipose
39	chr12:48526400-48540200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:48526400-48543600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:48527000-48536600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:48527200-48538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr12:48527600-48535000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:48528200-48535800	Weak transcription	Primary B cells from cord blood	blood
45	chr12:48528800-48532000	Weak transcription	Psoas Muscle	Psoas
46	chr12:48528800-48533000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:48529200-48533000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:48529200-48533200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:48529200-48535400	Weak transcription	Small Intestine	intestine
50	chr12:48529200-48536400	Weak transcription	Monocytes-CD14+_RO01746	blood

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