Variant report

Variant	rs775241
Chromosome Location	chr12:57936327-57936328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57934862..57936382-chr12:58129218..58130903,2	K562	blood:
2	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:

Variant related genes	Relation type
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1148552	0.97[MKK][hapmap]
rs1148553	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1148554	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148555	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1284465	0.87[EUR][1000 genomes]
rs1284605	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299737	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1629410	0.88[EUR][1000 genomes]
rs1669294	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669296	0.92[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678537	0.92[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1679368	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709871	0.85[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs1709874	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2127318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2620677	0.83[EUR][1000 genomes]
rs2620679	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2672571	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs2928382	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2943696	0.84[EUR][1000 genomes]
rs3782129	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474544	0.84[EUR][1000 genomes]
rs4760273	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs496245	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs511752	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs542278	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs697221	0.92[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703836	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs703838	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs703839	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7299631	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs747340	0.88[EUR][1000 genomes]
rs775236	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs775237	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775323	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs775324	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776038	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs776039	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964074	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs796546	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969683	0.83[ASN][1000 genomes]
rs899653	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs9737891	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
2	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs775241	AVIL	cis	cerebellum	SCAN
rs775241	KRT81	cis	parietal	SCAN
rs775241	ATF7	cis	cerebellum	SCAN
rs775241	ITGB7	cis	cerebellum	SCAN
rs775241	KRT7	cis	cerebellum	SCAN
rs775241	ACVRL1	cis	cerebellum	SCAN
rs775241	CALCOCO1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57918600-57936400	Strong transcription	Brain Inferior Temporal Lobe	brain
3	chr12:57918600-57939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:57919000-57937400	Weak transcription	Right Atrium	heart
5	chr12:57919200-57939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:57919400-57936400	Strong transcription	Primary B cells from peripheral blood	blood
7	chr12:57919400-57936800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:57919400-57937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:57919400-57939400	Strong transcription	Fetal Stomach	stomach
10	chr12:57919800-57937000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:57919800-57937800	Strong transcription	Fetal Intestine Small	intestine
12	chr12:57920000-57936400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:57920000-57937800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:57920200-57936800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:57920200-57937400	Strong transcription	Fetal Brain Female	brain
16	chr12:57920400-57936800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:57920400-57938600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:57920600-57938800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:57920800-57937000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:57920800-57937200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:57921000-57938800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:57921200-57938600	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:57921400-57939600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:57921800-57937400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:57923000-57939800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:57923200-57936800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:57923400-57937800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:57924200-57937600	Strong transcription	Placenta	Placenta
29	chr12:57924400-57937400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:57927200-57937200	Weak transcription	Fetal Heart	heart
31	chr12:57927200-57939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:57928400-57937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:57928400-57937400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:57928400-57937600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:57928400-57939600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:57929000-57937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:57929000-57939400	Weak transcription	Small Intestine	intestine
38	chr12:57929000-57939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:57929400-57939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:57929600-57939600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:57929600-57939600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:57929800-57937400	Weak transcription	Brain Anterior Caudate	brain
43	chr12:57931200-57936400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:57931200-57936400	Strong transcription	Adipose Nuclei	Adipose
45	chr12:57931600-57939200	Strong transcription	A549	lung
46	chr12:57931800-57936400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:57931800-57936600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:57932600-57939600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:57932800-57939600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr12:57932800-57939600	Weak transcription	Psoas Muscle	Psoas

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