Variant report

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172893225..172894892-chr2:172895220..172897617,2	MCF-7	breast:
2	chr2:172863330..172866297-chr2:172895128..172896991,2	K562	blood:
3	chr2:172895443..172898175-chr2:172947631..172951395,3	MCF-7	breast:
4	chr2:172889595..172892508-chr2:172896420..172898140,2	K562	blood:
5	chr2:172894437..172897042-chr2:172954737..172956688,2	MCF-7	breast:
6	chr2:172892888..172895304-chr2:172895689..172897604,2	K562	blood:
7	chr2:172896231..172898804-chr2:172903539..172906403,3	K562	blood:
8	chr2:172895941..172897535-chr2:172913713..172916052,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METAP1D-2	chr2:172896324-172897114	l_1987_chr2:172825346-172897114_testes

No data

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11673986	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11675404	0.82[ASW][hapmap]
rs11681005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11688839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695630	0.82[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap]
rs12988345	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988675	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989544	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13013988	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs17500199	0.85[JPT][hapmap]
rs1965159	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56041936	0.83[EUR][1000 genomes]
rs62183803	0.82[EUR][1000 genomes]
rs62183807	0.84[EUR][1000 genomes]
rs62183812	0.84[EUR][1000 genomes]
rs62183813	0.83[EUR][1000 genomes]
rs7580363	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12996935	B3GALT1	cis	cerebellum	SCAN
rs12996935	SLC25A12	cis	cerebellum	SCAN
rs12996935	MAP1D	cis	parietal	SCAN
rs12996935	SLC25A12	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172878600-172898200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:172887400-172902800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:172893600-172902000	Weak transcription	K562	blood
5	chr2:172895600-172897600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:172896000-172897200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:172896200-172897000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:172896600-172897000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:172896600-172897000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:172896600-172897000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:172896600-172897000	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:172896800-172897000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:172896800-172897000	Enhancers	Psoas Muscle	Psoas
14	chr2:172896800-172897000	Enhancers	Spleen	Spleen

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