Variant report

Variant	rs9888418
Chromosome Location	chr12:1840561-1840562
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	chr12:1838787..1840977-chr12:1852855..1855148,3	K562	blood:
2	chr12:1799601..1802514-chr12:1838626..1842574,3	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1058322	0.85[ASN][1000 genomes]
rs10735000	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744548	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10744549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773979	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10773981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773987	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848554	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832522	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12296831	0.86[EUR][1000 genomes]
rs1468491	0.81[EUR][1000 genomes]
rs16928751	0.81[EUR][1000 genomes]
rs1860054	0.81[EUR][1000 genomes]
rs1860055	0.81[EUR][1000 genomes]
rs2058112	0.86[EUR][1000 genomes]
rs2286380	0.81[EUR][1000 genomes]
rs35854772	0.81[EUR][1000 genomes]
rs4766414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57216374	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60523400	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66673051	0.81[EUR][1000 genomes]
rs67365540	0.81[EUR][1000 genomes]
rs67405160	0.81[EUR][1000 genomes]
rs67567175	0.81[EUR][1000 genomes]
rs703176	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132184	0.81[EUR][1000 genomes]
rs73040178	0.81[EUR][1000 genomes]
rs73040720	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316374	0.81[EUR][1000 genomes]
rs7488369	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767870	0.98[ASN][1000 genomes]
rs7954991	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963224	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967137	0.81[EUR][1000 genomes]
rs7975375	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805042	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9805109	0.87[EUR][1000 genomes];0.98[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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1802400-1841200	Weak transcription	HMEC	breast
2	chr12:1806200-1844400	Weak transcription	NHEK	skin
3	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
4	chr12:1816200-1849400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
7	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
8	chr12:1816400-1841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:1816400-1841400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:1816600-1846200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:1817000-1856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:1823000-1866600	Weak transcription	Gastric	stomach
13	chr12:1824000-1849400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:1824000-1849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:1824000-1850400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:1824000-1866600	Weak transcription	HSMM	muscle
17	chr12:1824800-1846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:1824800-1849400	Weak transcription	Thymus	Thymus
19	chr12:1825000-1849000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:1825000-1849400	Weak transcription	Fetal Thymus	thymus
21	chr12:1825200-1846600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:1825200-1850200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:1825200-1855400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:1826000-1846800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:1826000-1849200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:1826000-1885400	Weak transcription	NH-A	brain
27	chr12:1826200-1846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:1826200-1849400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:1826200-1849600	Weak transcription	A549	lung
30	chr12:1826400-1846800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:1826400-1849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:1828600-1855800	Weak transcription	Fetal Intestine Large	intestine
33	chr12:1828800-1847200	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:1829200-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:1829200-1849400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:1830000-1841600	Weak transcription	Stomach Mucosa	stomach
37	chr12:1830000-1847000	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:1831200-1849400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:1831200-1850000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:1831400-1849400	Weak transcription	Hela-S3	cervix
41	chr12:1831400-1857800	Weak transcription	Lung	lung
42	chr12:1831600-1840600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:1831600-1846800	Weak transcription	Right Atrium	heart
44	chr12:1832000-1841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:1833200-1842000	Weak transcription	Dnd41	blood
46	chr12:1833200-1846000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:1833200-1846200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:1834200-1842000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:1834400-1850600	Weak transcription	Osteobl	bone
50	chr12:1835600-1842800	Enhancers	HepG2	liver

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