Variant report

Variant	rs7300410
Chromosome Location	chr12:30898946-30898947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:30896873..30900728-chr12:30906376..30910229,3	MCF-7	breast:
2	chr12:30897584..30899613-chr12:30901110..30903756,2	K562	blood:
3	chr12:30897584..30899597-chr12:30900908..30902610,2	K562	blood:
4	chr12:30898396..30901084-chr12:30906438..30909429,2	K562	blood:

Variant related genes	Relation type
ENSG00000110888	Chromatin interaction
ENSG00000246331	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11608803	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11613738	1.00[MEX][hapmap]
rs12314492	0.88[AMR][1000 genomes]
rs1485346	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1560019	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17486840	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17560141	1.00[ASN][1000 genomes]
rs17687472	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17687791	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17687846	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17687964	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17688437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17739338	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs2099029	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2882856	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4459394	1.00[ASN][1000 genomes]
rs4930937	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4931357	1.00[ASN][1000 genomes]
rs4931358	1.00[ASN][1000 genomes]
rs4931359	1.00[ASN][1000 genomes]
rs4931363	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55957969	1.00[ASN][1000 genomes]
rs73077865	1.00[ASN][1000 genomes]
rs73077869	1.00[ASN][1000 genomes]
rs73077870	1.00[ASN][1000 genomes]
rs73077877	1.00[ASN][1000 genomes]
rs73077884	1.00[ASN][1000 genomes]
rs73077887	1.00[ASN][1000 genomes]
rs73077893	1.00[ASN][1000 genomes]
rs73079959	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079962	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079965	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079966	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079970	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079971	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73079992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079995	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079996	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73082005	0.88[AMR][1000 genomes]
rs73082008	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73082068	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7300410	CAPRIN2	cis	cerebellum	SCAN
rs7300410	CAPRIN2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
3	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
4	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:30864600-30905200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:30871400-30900800	Weak transcription	K562	blood
7	chr12:30872200-30903800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:30872400-30903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:30874600-30899000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:30876000-30906600	Weak transcription	Fetal Intestine Small	intestine
11	chr12:30878000-30899200	Weak transcription	Fetal Brain Male	brain
12	chr12:30878000-30904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:30878000-30904400	Weak transcription	Pancreas	Pancrea
14	chr12:30878200-30906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:30878800-30906600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:30879600-30899400	Weak transcription	NHDF-Ad	bronchial
17	chr12:30879800-30905800	Weak transcription	NHLF	lung
18	chr12:30882000-30899200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:30882000-30899200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:30882000-30906800	Weak transcription	Psoas Muscle	Psoas
21	chr12:30882200-30899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:30882200-30899200	Weak transcription	Aorta	Aorta
23	chr12:30882200-30905600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:30882200-30905800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:30882200-30906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:30882200-30906400	Weak transcription	Lung	lung
27	chr12:30882200-30906400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:30882200-30906600	Weak transcription	Placenta	Placenta
29	chr12:30882200-30906800	Weak transcription	Esophagus	oesophagus
30	chr12:30882400-30905400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:30882400-30906600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:30882600-30905400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:30882600-30906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:30882600-30906400	Weak transcription	Right Ventricle	heart
35	chr12:30882800-30906800	Weak transcription	Gastric	stomach
36	chr12:30883000-30899000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:30883200-30905800	Weak transcription	HSMMtube	muscle
38	chr12:30883200-30906400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:30884800-30905800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:30885000-30905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:30886400-30899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:30886600-30899200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:30886600-30906400	Weak transcription	Brain Substantia Nigra	brain
44	chr12:30886800-30899000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:30886800-30899200	Weak transcription	Brain Anterior Caudate	brain
46	chr12:30886800-30905800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:30887000-30899200	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:30888200-30899200	Weak transcription	HSMM	muscle
49	chr12:30888400-30899200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:30888400-30906800	Weak transcription	Fetal Intestine Large	intestine

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