Variant report

Variant	rs4652362
Chromosome Location	chr1:179268323-179268324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179261421..179263991-chr1:179268022..179270344,2	K562	blood:
2	chr1:179266790..179268502-chr1:179273763..179275636,2	K562	blood:
3	chr1:179260118..179263991-chr1:179268022..179270892,4	K562	blood:

Variant related genes	Relation type
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10913709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913717	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913726	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913769	1.00[CHB][hapmap]
rs11581659	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12061572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066392	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135682	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722736	1.00[CHB][hapmap]
rs12730051	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730056	1.00[ASW][hapmap];0.90[LWK][hapmap]
rs12746331	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12755434	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756624	0.80[AFR][1000 genomes]
rs17277834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248818	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484442	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493120	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34315375	0.88[ASN][1000 genomes]
rs34727092	0.82[EUR][1000 genomes]
rs4651023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425536	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs68039464	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4652362	FAM5B	cis	parietal	SCAN
rs4652362	NPHS2	cis	cerebellum	SCAN
rs4652362	TOR3A	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179268400	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:179263800-179304600	Weak transcription	Lung	lung
3	chr1:179263800-179306400	Weak transcription	Gastric	stomach
4	chr1:179264000-179271400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:179264000-179279600	Weak transcription	Fetal Brain Male	brain
6	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
7	chr1:179264400-179271400	Weak transcription	Left Ventricle	heart
8	chr1:179264600-179268400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:179264600-179271400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:179264600-179271400	Weak transcription	Fetal Stomach	stomach
11	chr1:179264600-179271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:179264600-179271600	Weak transcription	Psoas Muscle	Psoas
13	chr1:179264600-179271600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:179264600-179272000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:179264600-179272800	Weak transcription	Fetal Lung	lung
16	chr1:179264600-179273400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:179264600-179273400	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:179264600-179274200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:179264600-179275000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:179264600-179278600	Weak transcription	Colonic Mucosa	Colon
21	chr1:179264600-179281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
24	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
26	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:179264800-179270400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:179264800-179271400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:179264800-179271400	Weak transcription	Fetal Intestine Large	intestine
30	chr1:179264800-179271600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:179264800-179271600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:179264800-179271600	Weak transcription	HMEC	breast
33	chr1:179264800-179271800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:179264800-179271800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:179264800-179272000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:179264800-179272000	Weak transcription	Brain Anterior Caudate	brain
37	chr1:179264800-179272000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:179264800-179272000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:179264800-179272200	Weak transcription	Adipose Nuclei	Adipose
40	chr1:179264800-179272200	Weak transcription	HSMM	muscle
41	chr1:179264800-179272200	Weak transcription	NHLF	lung
42	chr1:179264800-179273400	Weak transcription	Ovary	ovary
43	chr1:179264800-179276200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:179264800-179276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:179264800-179277800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:179264800-179278800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:179264800-179279400	Weak transcription	HSMMtube	muscle
48	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
50	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon

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