Variant report

Variant	rs4717331
Chromosome Location	chr7:66378886-66378887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr7:66378619-66378914	A549	lung:	n/a	n/a
2	NR3C1	chr7:66378620-66378921	A549	lung:	n/a	n/a
3	FOXA1	chr7:66378629-66378906	HepG2	liver:	n/a	n/a
4	FOXA1	chr7:66378636-66378919	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66378566..66381625-chr7:66385153..66387745,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179131	TF binding region
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10235423	0.80[YRI][hapmap]
rs10267335	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10281796	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12530806	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12536410	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12698546	0.86[EUR][1000 genomes]
rs12698547	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13220977	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13227468	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13231140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28441684	0.83[EUR][1000 genomes]
rs28648401	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901311	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34577323	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3800817	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4717328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718412	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718422	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718430	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68168107	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4717331	CRCP	cis	parietal	SCAN
rs4717331	GUSB	cis	cerebellum	SCAN
rs4717331	GUSB	cis	parietal	SCAN
rs4717331	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4717331	RP4-756H11.3	cis	lung	GTEx
rs4717331	CRCP	cis	cerebellum	SCAN
rs4717331	ASL	cis	multi-tissue	Pritchard
rs4717331	RP4-756H11.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:66350600-66385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:66353200-66379600	Weak transcription	GM12878-XiMat	blood
5	chr7:66364400-66385400	Weak transcription	HSMMtube	muscle
6	chr7:66364800-66385000	Weak transcription	Brain Anterior Caudate	brain
7	chr7:66366400-66385600	Weak transcription	Brain Substantia Nigra	brain
8	chr7:66368000-66385400	Weak transcription	Adipose Nuclei	Adipose
9	chr7:66369000-66385400	Weak transcription	Thymus	Thymus
10	chr7:66369000-66385600	Weak transcription	Ovary	ovary
11	chr7:66370000-66385200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:66370200-66385400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:66370800-66385000	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:66371000-66385200	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:66371200-66382000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:66371200-66385400	Weak transcription	Fetal Intestine Small	intestine
17	chr7:66371200-66385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:66371800-66382400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:66371800-66385400	Weak transcription	Fetal Stomach	stomach
20	chr7:66373000-66382600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:66376800-66379000	Enhancers	HepG2	liver
22	chr7:66377400-66381800	Weak transcription	Liver	Liver
23	chr7:66378400-66379400	Enhancers	A549	lung
24	chr7:66378600-66379400	Enhancers	K562	blood
25	chr7:66378800-66379000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:66378800-66379000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:66378800-66379000	Enhancers	HUES6 Cell Line	embryonic stem cell

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