Variant report

Variant	rs6945788
Chromosome Location	chr7:108254484-108254485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108209177..108212583-chr7:108250280..108255068,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB9-1	chr7:108254377-108254711	ENSG00000225647

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1029707	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1029708	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11767037	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11767071	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11773524	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11773875	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17341955	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17426638	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108731	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2215141	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34505662	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4298438	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55760662	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58954269	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466244	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67940245	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949766	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951751	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs726608	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs727881	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7790890	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7795236	0.83[EUR][1000 genomes]
rs9690171	0.85[EUR][1000 genomes]
rs975124	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9768342	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9918599	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1792680	chr7:108246985-108254739	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv275371	chr7:108250854-108257413	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6945788	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108249200-108254800	Enhancers	Liver	Liver
2	chr7:108252000-108255000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:108252200-108255000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:108253800-108255400	Enhancers	HepG2	liver
5	chr7:108254000-108254600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:108254000-108254600	Enhancers	Rectal Smooth Muscle	rectum
7	chr7:108254000-108254800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:108254000-108254800	Enhancers	Colon Smooth Muscle	Colon
9	chr7:108254000-108255400	Enhancers	Fetal Lung	lung
10	chr7:108254000-108255600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr7:108254000-108255600	Enhancers	Fetal Kidney	kidney
12	chr7:108254200-108255000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:108254200-108255400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr7:108254200-108255600	Active TSS	Brain Germinal Matrix	brain
15	chr7:108254200-108255800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr7:108254200-108258000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:108254200-108258600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:108254400-108255600	Enhancers	Fetal Brain Male	brain
19	chr7:108254400-108255800	Enhancers	HUES48 Cell Line	embryonic stem cell

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