Variant report

Variant	rs405212
Chromosome Location	chr3:191119818-191119819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:191114086..191115834-chr3:191118991..191121989,2	K562	blood:
2	chr3:191119634..191120179-chrX:94170167..94170669,2	MCF-7	breast:
3	chr3:191113983..191115834-chr3:191118918..191120491,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1473867	0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1473868	0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1662182	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs167151	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs167152	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1708285	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176825	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs184141	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293377	0.86[CHD][hapmap]
rs293838	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293853	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs366757	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383437	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs385582	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538465	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs542437	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55827603	0.84[ASN][1000 genomes]
rs59855028	0.84[ASN][1000 genomes]
rs697909	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs697910	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs697911	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs405212	TCTEX1D2	cis	cerebellum	SCAN
rs405212	CCDC50	cis	parietal	SCAN
rs405212	NCCRP1	trans	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
3	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
5	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
7	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
8	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:191114400-191120400	Weak transcription	HSMM	muscle
11	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:191114400-191121400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:191116000-191121200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:191116000-191121600	Weak transcription	Primary B cells from cord blood	blood
15	chr3:191117200-191127200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:191117200-191127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:191118000-191121000	Weak transcription	HUVEC	blood vessel
18	chr3:191118200-191120000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:191118200-191127200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:191118400-191130000	Weak transcription	NH-A	brain
21	chr3:191119400-191120000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:191119400-191120000	Strong transcription	HSMMtube	muscle
23	chr3:191119400-191120200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:191119600-191120000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:191119600-191120000	Enhancers	K562	blood
26	chr3:191119800-191120000	Enhancers	Left Ventricle	heart
27	chr3:191119800-191120000	Enhancers	Ovary	ovary

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