Variant report

Variant	rs7650345
Chromosome Location	chr3:134655446-134655447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1020434	1.00[JPT][hapmap]
rs13353524	1.00[JPT][hapmap]
rs1350350	1.00[JPT][hapmap]
rs16842415	1.00[JPT][hapmap]
rs16842453	1.00[JPT][hapmap]
rs16842468	1.00[JPT][hapmap]
rs17203924	1.00[JPT][hapmap]
rs187585	1.00[JPT][hapmap]
rs253878	1.00[JPT][hapmap]
rs253880	1.00[JPT][hapmap]
rs28223	1.00[JPT][hapmap]
rs36059	1.00[JPT][hapmap]
rs36062	1.00[JPT][hapmap]
rs36063	1.00[JPT][hapmap]
rs36074	1.00[JPT][hapmap]
rs36097	1.00[JPT][hapmap]
rs36102	1.00[JPT][hapmap]
rs36109	1.00[JPT][hapmap]
rs36110	1.00[JPT][hapmap]
rs36111	1.00[JPT][hapmap]
rs36112	1.00[JPT][hapmap]
rs36114	1.00[JPT][hapmap]
rs36115	1.00[JPT][hapmap]
rs36116	1.00[JPT][hapmap]
rs36117	1.00[JPT][hapmap]
rs36121	1.00[JPT][hapmap]
rs36123	1.00[JPT][hapmap]
rs36124	1.00[JPT][hapmap]
rs36174	0.91[TSI][hapmap]
rs36175	0.91[TSI][hapmap]
rs3853726	1.00[JPT][hapmap]
rs39698	1.00[JPT][hapmap]
rs39699	1.00[JPT][hapmap]
rs40524	1.00[JPT][hapmap]
rs41182	1.00[JPT][hapmap]
rs4955533	1.00[JPT][hapmap]
rs574719	1.00[JPT][hapmap]
rs6776069	1.00[JPT][hapmap]
rs6788931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289488	1.00[JPT][hapmap]
rs9832922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855772	1.00[JPT][hapmap]
rs9866987	1.00[JPT][hapmap]
rs9874260	0.82[CHD][hapmap]
rs9876803	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7650345	EPHB1	cis	multi-tissue	Pritchard
rs7650345	CRYAA	trans	cerebellum	SCAN
rs7650345	EPHB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134644600-134656400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:134649000-134656200	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:134649000-134656200	Weak transcription	Fetal Stomach	stomach
4	chr3:134650400-134656000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:134650600-134655600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:134650600-134655600	Weak transcription	GM12878-XiMat	blood
7	chr3:134650600-134660600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:134651200-134655800	Weak transcription	Fetal Brain Male	brain
9	chr3:134653000-134656200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:134653200-134657600	Enhancers	Brain Anterior Caudate	brain
11	chr3:134653400-134655800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:134653400-134657200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:134653800-134659000	Enhancers	Brain Germinal Matrix	brain
14	chr3:134654000-134655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:134654000-134656200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:134654200-134657400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:134654400-134656400	Weak transcription	Right Atrium	heart
18	chr3:134654600-134658200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:134654800-134657200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:134654800-134658800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:134655000-134659400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:134655200-134655800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
23	chr3:134655200-134657200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:134655400-134655800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr3:134655400-134657000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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