Variant report

Variant	rs9683795
Chromosome Location	chr4:7800345-7800346
allele	C/T
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	CEBPB	chr4:7800044-7800379	IMR90	lung:	n/a	n/a
2	NFYB	chr4:7799600-7800399	K562	blood:	n/a	chr4:7799806-7799821
3	NFYB	chr4:7799553-7800582	Hela-S3	cervix:	n/a	chr4:7799806-7799821
4	SP1	chr4:7799637-7800416	A549	lung:	n/a	n/a
5	SP1	chr4:7799784-7800345	H1-hESC	embryonic stem cell:	n/a	n/a
6	NFYA	chr4:7799443-7800428	Hela-S3	cervix:	n/a	n/a
7	SP1	chr4:7799577-7800400	K562	blood:	n/a	n/a
8	SP1	chr4:7799915-7800395	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFYB	chr4:7799622-7800463	GM12878	blood:	n/a	chr4:7799806-7799821
10	POLR2A	chr4:7799396-7801058	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7799366..7802066-chr4:7938906..7941900,2	MCF-7	breast:

Variant related genes	Relation type
AFAP1	TF binding region
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10440168	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733791	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11734524	0.81[CHB][hapmap]
rs11933506	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs11938080	0.89[EUR][1000 genomes]
rs13119259	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13127069	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13128692	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17770147	0.82[YRI][hapmap]
rs17770177	0.82[YRI][hapmap]
rs2269852	0.86[CHB][hapmap]
rs2269874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4274845	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296663	0.82[YRI][hapmap]
rs4411970	0.82[YRI][hapmap]
rs4689864	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689865	1.00[YRI][hapmap]
rs4689868	1.00[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446623	0.82[CEU][hapmap]
rs6814649	0.82[YRI][hapmap]
rs6824266	0.82[YRI][hapmap]
rs6826354	0.82[YRI][hapmap]
rs6829537	0.82[YRI][hapmap]
rs6839128	0.85[YRI][hapmap]
rs6839744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845014	0.82[YRI][hapmap]
rs6848279	0.82[YRI][hapmap]
rs6848487	0.82[YRI][hapmap]
rs6856371	1.00[YRI][hapmap]
rs6856795	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9683795	GRPEL1	cis	cerebellum	SCAN
rs9683795	AFAP1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
7	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
8	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
11	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
13	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
14	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:7786000-7800800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:7790800-7800800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:7790800-7803600	Strong transcription	HSMM	muscle
22	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
24	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:7791200-7800800	Weak transcription	Spleen	Spleen
26	chr4:7791400-7800400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:7791600-7800400	Weak transcription	Left Ventricle	heart
29	chr4:7791600-7800400	Weak transcription	Right Ventricle	heart
30	chr4:7791600-7801200	Weak transcription	Fetal Brain Male	brain
31	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:7792600-7803400	Strong transcription	A549	lung
34	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
35	chr4:7793200-7803800	Strong transcription	NH-A	brain
36	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:7794800-7803400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:7795600-7800600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:7795600-7803800	Weak transcription	Fetal Kidney	kidney
40	chr4:7795800-7803800	Weak transcription	Fetal Heart	heart
41	chr4:7796000-7800400	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:7796000-7803400	Strong transcription	HUVEC	blood vessel
43	chr4:7796600-7803400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:7796800-7804200	Strong transcription	NHEK	skin
45	chr4:7797000-7807000	Weak transcription	Liver	Liver
46	chr4:7797200-7803000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:7797200-7803800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr4:7797600-7800400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:7797600-7802400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr4:7797600-7802800	Strong transcription	Rectal Mucosa Donor 29	rectum

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