Variant report

Variant	rs12230349
Chromosome Location	chr12:1826661-1826662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1815063..1817215-chr12:1824872..1827970,3	K562	blood:
2	chr12:1771225..1773425-chr12:1825793..1828213,2	K562	blood:
3	chr12:1824311..1826936-chr12:1833466..1835089,2	K562	blood:
4	chr12:1805534..1808436-chr12:1826572..1828951,2	K562	blood:
5	chr12:1825414..1827008-chr12:1830876..1832417,2	K562	blood:

Variant related genes	Relation type
ENSG00000271500	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10491959	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848555	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061928	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061929	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061931	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061932	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061934	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061941	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061943	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061944	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061947	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11061949	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061950	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061951	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061953	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061954	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061955	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061958	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061959	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061963	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061975	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11061979	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610397	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11610411	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11610838	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11612238	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612726	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11613594	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11614622	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12229999	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230994	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16928662	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16928665	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286382	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2369975	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58500393	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61153802	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6489322	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1045312	chr12:1805856-1843202	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:1802400-1841200	Weak transcription	HMEC	breast
5	chr12:1806000-1840000	Weak transcription	Spleen	Spleen
6	chr12:1806200-1844400	Weak transcription	NHEK	skin
7	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
8	chr12:1808400-1830800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:1815200-1827800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:1816200-1836400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:1816200-1849400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
14	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
15	chr12:1816400-1840200	Weak transcription	Colonic Mucosa	Colon
16	chr12:1816400-1841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:1816400-1841400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:1816600-1827600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:1816600-1846200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:1817000-1835200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:1817000-1856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:1819200-1833800	Enhancers	Liver	Liver
23	chr12:1819800-1827200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:1820200-1832400	Weak transcription	Primary T cells from cord blood	blood
25	chr12:1820400-1827800	Weak transcription	Small Intestine	intestine
26	chr12:1820400-1828000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:1821400-1827800	Weak transcription	Fetal Lung	lung
28	chr12:1821400-1827800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:1821400-1830800	Weak transcription	Hela-S3	cervix
30	chr12:1821600-1827800	Weak transcription	Right Ventricle	heart
31	chr12:1822200-1827800	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:1822200-1827800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:1822400-1827800	Weak transcription	Psoas Muscle	Psoas
34	chr12:1822400-1827800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:1822400-1838600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:1822600-1830200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:1823000-1866600	Weak transcription	Gastric	stomach
38	chr12:1823600-1828800	Weak transcription	Left Ventricle	heart
39	chr12:1823800-1831000	Weak transcription	Lung	lung
40	chr12:1824000-1849400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:1824000-1849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:1824000-1850400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:1824000-1866600	Weak transcription	HSMM	muscle
44	chr12:1824200-1827800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:1824200-1833600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:1824400-1833600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:1824600-1827800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:1824800-1828200	Weak transcription	Dnd41	blood
49	chr12:1824800-1828600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:1824800-1835800	Weak transcription	Primary hematopoietic stem cells	blood

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