Variant report

Variant	rs7806407
Chromosome Location	chr7:7985866-7985867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7985394..7987246-chr7:8007323..8009239,2	K562	blood:
2	chr7:7982231..7984516-chr7:7984634..7987020,2	MCF-7	breast:
3	chr7:7985182..7986874-chr7:7992150..7994347,2	K562	blood:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10272483	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538224	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231445	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041567	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34768970	1.00[ASN][1000 genomes]
rs37943	1.00[ASN][1000 genomes]
rs37946	1.00[ASN][1000 genomes]
rs37953	1.00[ASN][1000 genomes]
rs6463751	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6947392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951010	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975902	0.91[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6976735	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718549	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73359459	1.00[ASN][1000 genomes]
rs73359463	1.00[ASN][1000 genomes]
rs7779286	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690117	0.83[AMR][1000 genomes]
rs9690598	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv525502	chr7:7938596-7996590	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv606048	chr7:7938596-7996590	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7806407	Contig43410_RC	trans	multi-tissue	Pritchard
rs7806407	AC009473.1	cis	Thyroid	GTEx
rs7806407	CASZ1	cis	Liver	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7976000-7986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:7976800-7986200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:7984200-7987200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:7984400-7986000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:7984400-7995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:7984400-7996200	Weak transcription	Left Ventricle	heart
7	chr7:7984600-7986200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:7984800-7986000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:7984800-7986600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:7984800-7996800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:7985000-7986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:7985000-7986400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:7985000-7987000	Enhancers	Thymus	Thymus
14	chr7:7985000-7991200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:7985000-8003800	Weak transcription	Primary B cells from cord blood	blood
16	chr7:7985200-7986200	Enhancers	GM12878-XiMat	blood
17	chr7:7985200-7986800	Enhancers	Fetal Thymus	thymus
18	chr7:7985400-7986800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:7985400-8007600	Weak transcription	Psoas Muscle	Psoas
20	chr7:7985600-7990400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:7985800-7986000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:7985800-7986600	Weak transcription	Placenta	Placenta
23	chr7:7985800-7986800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr7:7985800-7990200	Enhancers	Dnd41	blood

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