Variant report

Variant	rs2529190
Chromosome Location	chr7:101341246-101341247
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	chr7:101338468..101347550-chr7:101456060..101461227,20	MCF-7	breast:
2	chr7:101339145..101341455-chr7:101342209..101344273,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12534998	0.92[ASN][1000 genomes]
rs12535663	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1722207	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1965519	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs1969432	0.81[ASN][1000 genomes]
rs2429068	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2529179	0.89[ASN][1000 genomes]
rs2529181	0.85[ASN][1000 genomes]
rs2529182	0.89[ASN][1000 genomes]
rs2529185	0.95[CHB][hapmap]
rs2529186	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2529187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529188	0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2529189	0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2529238	0.81[CHB][hapmap]
rs2529242	0.85[ASN][1000 genomes]
rs2529243	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs2529246	0.89[ASN][1000 genomes]
rs2529247	0.94[ASN][1000 genomes]
rs2690887	0.80[CHB][hapmap]
rs2690890	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2690891	0.89[ASN][1000 genomes]
rs2690892	0.89[ASN][1000 genomes]
rs2690893	0.89[ASN][1000 genomes]
rs2690896	0.93[ASN][1000 genomes]
rs2690902	0.98[ASN][1000 genomes]
rs940479	0.87[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	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv831079	chr7:101273495-101466776	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2529190	TAF6	cis	parietal	SCAN
rs2529190	BAIAP2L1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101332000-101376800	Weak transcription	Right Atrium	heart
2	chr7:101337400-101342800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:101338000-101342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:101340000-101342200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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