Variant report

Variant	rs1316488
Chromosome Location	chr2:112909143-112909144
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	chr2:112905095..112907342-chr2:112908962..112911780,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10189625	0.85[JPT][hapmap]
rs10196498	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10207420	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123128	0.92[JPT][hapmap]
rs11675443	0.92[JPT][hapmap]
rs1320360	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312697	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4318395	0.84[JPT][hapmap]
rs4411701	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4848272	0.92[JPT][hapmap]
rs4849045	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849046	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849048	0.85[JPT][hapmap];0.80[TSI][hapmap]
rs6542041	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755850	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7571942	1.00[CEU][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7575979	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593053	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[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];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7607362	1.00[CEU][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers 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 target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1316488	PSD4	cis	parietal	SCAN
rs1316488	POLR1B	cis	parietal	SCAN
rs1316488	FBLN7	cis	cerebellum	SCAN
rs1316488	POLR1B	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112896400-112934600	Weak transcription	Aorta	Aorta
2	chr2:112898200-112915000	Weak transcription	Pancreas	Pancrea
3	chr2:112899000-112913000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:112899200-112914000	Weak transcription	HepG2	liver
5	chr2:112900200-112913600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:112900600-112931400	Weak transcription	Fetal Lung	lung
7	chr2:112900800-112912800	Weak transcription	Spleen	Spleen
8	chr2:112904800-112911600	Enhancers	NHDF-Ad	bronchial
9	chr2:112905000-112910800	Enhancers	Osteobl	bone
10	chr2:112905400-112911600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:112906200-112909800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:112906200-112911400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:112906800-112909200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:112906800-112910000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:112906800-112912800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:112907000-112909200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:112907000-112909400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:112907200-112909600	Weak transcription	Fetal Stomach	stomach
19	chr2:112907200-112920400	Weak transcription	Right Atrium	heart
20	chr2:112907400-112909200	Enhancers	NHLF	lung
21	chr2:112907400-112909400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:112907400-112914200	Enhancers	HSMM	muscle
23	chr2:112907600-112914400	Enhancers	HSMMtube	muscle
24	chr2:112907800-112912000	Weak transcription	Right Ventricle	heart
25	chr2:112908000-112913000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:112908400-112909200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:112908400-112912200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:112908400-112912200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:112908400-112914000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:112908600-112911000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:112908600-112912200	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:112908800-112909200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:112908800-112910000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:112908800-112910000	Weak transcription	Adipose Nuclei	Adipose
35	chr2:112908800-112913000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:112908800-112913000	Weak transcription	HUVEC	blood vessel
37	chr2:112908800-112913200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:112908800-112913800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:112908800-112914000	Weak transcription	HMEC	breast
40	chr2:112909000-112910200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:112909000-112910800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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