Variant report

Variant	rs12821401
Chromosome Location	chr12:1878392-1878393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:1806785..1809377-chr12:1875667..1878614,2	K562	blood:
2	chr12:1869685..1874044-chr12:1876530..1880194,4	K562	blood:
3	chr12:1859249..1861989-chr12:1877875..1880136,2	MCF-7	breast:
4	chr12:1877724..1879451-chr12:1881713..1884446,2	MCF-7	breast:
5	chr12:1806568..1808285-chr12:1875506..1878614,3	K562	blood:
6	chr12:1877747..1879413-chr12:1888732..1890364,2	MCF-7	breast:
7	chr12:1800061..1801858-chr12:1877724..1879510,3	MCF-7	breast:
8	chr12:1876589..1879499-chr20:46131096..46132611,2	MCF-7	breast:
9	chr12:1877224..1880546-chr12:1949279..1951143,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271500	Chromatin interaction
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1029629	0.80[CHB][hapmap]
rs10848551	0.83[CHB][hapmap]
rs10848566	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11061918	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11061925	0.80[CHB][hapmap]
rs11061927	0.80[CHB][hapmap]
rs11061935	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11061946	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11061952	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11061956	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11061962	0.80[CHB][hapmap]
rs11061967	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061973	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230440	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12579507	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12580035	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12581815	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12810020	0.80[CHB][hapmap]
rs16928704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058033	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2058035	0.80[CHB][hapmap]
rs2370055	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4766413	0.80[CHB][hapmap]
rs7132033	0.80[CHB][hapmap]
rs71454839	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297509	0.80[CHB][hapmap]
rs73040736	0.81[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	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
4	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
5	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	nsv1038425	chr12:1857052-1902302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12821401	AKAP3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
2	chr12:1826000-1885400	Weak transcription	NH-A	brain
3	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
5	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
6	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
8	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
9	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
12	chr12:1863000-1882000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:1864800-1879800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:1864800-1882200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:1864800-1885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:1865000-1885200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:1866800-1883000	Weak transcription	Fetal Heart	heart
18	chr12:1867000-1882000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:1867000-1882000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:1867200-1878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:1867200-1878600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:1867200-1878800	Weak transcription	Fetal Intestine Small	intestine
24	chr12:1867200-1878800	Weak transcription	Lung	lung
25	chr12:1867200-1879200	Weak transcription	Gastric	stomach
26	chr12:1867200-1879200	Weak transcription	Left Ventricle	heart
27	chr12:1867200-1880200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:1867200-1880200	Weak transcription	Esophagus	oesophagus
29	chr12:1867200-1880200	Weak transcription	Fetal Stomach	stomach
30	chr12:1867200-1880400	Weak transcription	Fetal Intestine Large	intestine
31	chr12:1867200-1882000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:1867200-1882000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:1867200-1882000	Weak transcription	Thymus	Thymus
34	chr12:1867200-1883000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:1867200-1885600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:1867200-1888200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
38	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:1867600-1880000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:1867600-1882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:1867600-1882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:1867600-1882000	Weak transcription	Placenta	Placenta
43	chr12:1867600-1886800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:1867800-1885000	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:1868200-1882000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:1868400-1878800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:1868400-1879200	Weak transcription	Osteobl	bone
49	chr12:1868400-1882000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:1868400-1887000	Weak transcription	Primary hematopoietic stem cells	blood

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