Variant report

Variant	rs1709871
Chromosome Location	chr12:57903083-57903084
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57902587-57903358	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:57902874-57903254	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57903005-57903225	K562	blood:	n/a	n/a
4	POLR2A	chr12:57902939-57903201	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57883464..57886138-chr12:57902032..57904531,3	K562	blood:
2	chr12:57896366..57901111-chr12:57901647..57907518,8	K562	blood:
3	chr12:57881369..57883611-chr12:57902104..57905410,4	MCF-7	breast:
4	chr12:57901367..57904332-chr12:57904666..57906623,2	K562	blood:

No data

Variant related genes	Relation type
MARS	TF binding region
RN7SL312P	TF binding region
RNU6-594P	TF binding region
ENSG00000252865	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1148553	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1148554	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148555	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148557	0.85[ASW][hapmap];0.91[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1284465	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1284605	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1284606	0.91[AMR][1000 genomes]
rs1299737	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1617196	0.80[AMR][1000 genomes]
rs1629410	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669294	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669296	0.92[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669297	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678537	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1709874	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2127318	0.92[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2620677	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2620679	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs2672571	0.85[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs2673326	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2928382	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2943696	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782129	0.87[EUR][1000 genomes]
rs3847699	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs472895	0.87[AMR][1000 genomes]
rs474544	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760273	0.88[EUR][1000 genomes]
rs496245	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs508904	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs511752	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs541869	0.85[AMR][1000 genomes]
rs542278	0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs569251	0.87[AMR][1000 genomes]
rs697221	0.92[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs703835	0.85[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs703836	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs703837	0.85[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs703838	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs703839	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299631	0.87[EUR][1000 genomes]
rs747340	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775236	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775237	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs775241	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]
rs775323	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs775324	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs776038	0.92[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs776039	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7964074	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs796546	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7969683	0.88[EUR][1000 genomes]
rs899653	0.83[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs9737891	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	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
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats 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	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1709871	ACVRL1	cis	cerebellum	SCAN
rs1709871	RDH5	cis	cerebellum	SCAN
rs1709871	ITGA7	cis	cerebellum	SCAN
rs1709871	CALCOCO1	cis	cerebellum	SCAN
rs1709871	ATF7	cis	cerebellum	SCAN
rs1709871	AVIL	cis	cerebellum	SCAN
rs1709871	KRT7	cis	cerebellum	SCAN
rs1709871	DCTN2	cis	Muscle Skeletal	GTEx
rs1709871	STAT6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
3	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
4	chr12:57884000-57903200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
6	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
7	chr12:57892800-57908600	Weak transcription	Stomach Mucosa	stomach
8	chr12:57896200-57905400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:57896200-57905600	Weak transcription	NHDF-Ad	bronchial
10	chr12:57899000-57905200	Weak transcription	NHLF	lung
11	chr12:57899200-57905000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:57899600-57906400	Weak transcription	Small Intestine	intestine
13	chr12:57900000-57904600	Weak transcription	Right Ventricle	heart
14	chr12:57900000-57905000	Weak transcription	Gastric	stomach
15	chr12:57900000-57905200	Weak transcription	Colonic Mucosa	Colon
16	chr12:57900200-57904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:57900200-57905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:57900200-57905600	Weak transcription	Esophagus	oesophagus
19	chr12:57900400-57904000	Weak transcription	Pancreas	Pancrea
20	chr12:57900400-57904200	Weak transcription	Brain Anterior Caudate	brain
21	chr12:57900400-57904600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:57900400-57905000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:57900400-57905400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:57900400-57905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:57900400-57905400	Weak transcription	Ovary	ovary
26	chr12:57900400-57905600	Weak transcription	Fetal Brain Male	brain
27	chr12:57900600-57903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:57900600-57903200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:57900600-57903200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:57900600-57903200	Weak transcription	K562	blood
31	chr12:57900600-57903400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:57900600-57903600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:57900600-57903800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:57900600-57903800	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:57900600-57904400	Weak transcription	Spleen	Spleen
36	chr12:57900600-57904800	Weak transcription	Aorta	Aorta
37	chr12:57900600-57905000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:57900600-57905000	Weak transcription	Left Ventricle	heart
39	chr12:57900600-57905000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:57900600-57905000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:57900600-57905200	Weak transcription	Brain Angular Gyrus	brain
42	chr12:57900600-57905200	Weak transcription	Brain Substantia Nigra	brain
43	chr12:57900600-57905200	Weak transcription	Fetal Kidney	kidney
44	chr12:57900600-57905400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:57900600-57905800	Weak transcription	Psoas Muscle	Psoas
46	chr12:57900600-57912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:57900600-57912800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:57901600-57910600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:57901600-57911000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:57901600-57911800	Strong transcription	Lung	lung

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