Variant report

Variant	rs7690495
Chromosome Location	chr4:8046762-8046763
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	POLR2A	chr4:8046339-8046824	H1-neurons	neurons:	n/a	n/a
2	FOXA1	chr4:8046427-8046794	HepG2	liver:	n/a	chr4:8046616-8046631
3	KAP1	chr4:8046323-8046971	U2OS	brain:	n/a	n/a
4	KAP1	chr4:8046300-8046996	HEK293	kidney:	n/a	n/a
5	EBF1	chr4:8046481-8046855	GM12878	blood:	n/a	chr4:8046668-8046678 chr4:8046666-8046679 chr4:8046668-8046677 chr4:8046667-8046678
6	POLR2A	chr4:8046391-8046787	H1-neurons	neurons:	n/a	n/a
7	TCF7L2	chr4:8046273-8047004	HEK293	kidney:	n/a	n/a
8	FOXA1	chr4:8046355-8046769	HepG2	liver:	n/a	chr4:8046616-8046631
9	EBF1	chr4:8046473-8046825	GM12878	blood:	n/a	chr4:8046668-8046678 chr4:8046666-8046679 chr4:8046668-8046677 chr4:8046667-8046678

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8034679..8036492-chr4:8044258..8047037,2	K562	blood:

Variant related genes	Relation type
ABLIM2	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11947858	0.82[EUR][1000 genomes]
rs13109801	0.89[EUR][1000 genomes]
rs13115927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124344	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137881	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143861	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13146393	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13147575	0.83[EUR][1000 genomes]
rs17770936	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34067831	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34076429	0.80[EUR][1000 genomes]
rs34504352	0.82[EUR][1000 genomes]
rs57521485	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6852834	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214058	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv470009	chr4:8015421-8085174	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv878581	chr4:8021592-8100272	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878582	chr4:8023484-8047973	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv878583	chr4:8023484-8049713	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv878584	chr4:8023484-8075134	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv878585	chr4:8023484-8116202	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv878586	chr4:8023484-8148159	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv593624	chr4:8026176-8047973	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv878587	chr4:8031471-8075134	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv878588	chr4:8034772-8070793	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv878589	chr4:8034772-8089598	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7690495	GRPEL1	cis	parietal	SCAN
rs7690495	ACOX3	cis	lymphoblastoid	seeQTL
rs7690495	ACOX3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8010600-8052000	Weak transcription	Left Ventricle	heart
2	chr4:8031200-8052000	Weak transcription	Psoas Muscle	Psoas
3	chr4:8038000-8052000	Weak transcription	Right Ventricle	heart
4	chr4:8039200-8057000	Weak transcription	Gastric	stomach
5	chr4:8039400-8052400	Weak transcription	Pancreas	Pancrea
6	chr4:8039400-8056600	Weak transcription	Aorta	Aorta
7	chr4:8041200-8052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:8041800-8049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:8041800-8052000	Weak transcription	Adipose Nuclei	Adipose
10	chr4:8042000-8049200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:8042000-8049200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:8043200-8047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:8043200-8049800	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:8043400-8046800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:8044400-8048000	Strong transcription	Spleen	Spleen
16	chr4:8045400-8047000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr4:8045600-8052000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:8045800-8047000	Enhancers	Fetal Brain Male	brain
19	chr4:8046000-8047000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:8046000-8050800	Weak transcription	Esophagus	oesophagus
21	chr4:8046400-8047000	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:8046400-8047200	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr4:8046400-8048200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr4:8046600-8046800	Genic enhancers	Brain Angular Gyrus	brain
25	chr4:8046600-8046800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr4:8046600-8046800	Enhancers	Fetal Lung	lung
27	chr4:8046600-8046800	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr4:8046600-8047000	Enhancers	Brain Hippocampus Middle	brain
29	chr4:8046600-8047000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:8046600-8048000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr4:8046600-8052000	Weak transcription	Lung	lung

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