Variant report

Variant	rs28742899
Chromosome Location	chr4:649639-649640
allele	A/C
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	MAX	chr4:648843-650038	HepG2	liver:	n/a	chr4:649898-649905
2	BHLHE40	chr4:649464-649688	HepG2	liver:	n/a	n/a
3	MAX	chr4:649476-649681	K562	blood:	n/a	n/a
4	BHLHE40	chr4:649384-649973	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:649476-649808	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
2	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242686	TF binding region
ENSG00000133256	Chromatin interaction
ENSG00000242686	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10027549	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10027866	0.83[MKK][hapmap];0.81[TSI][hapmap]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119162	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28374488	0.80[AMR][1000 genomes]
rs28438498	0.85[MKK][hapmap];0.81[TSI][hapmap]
rs28470912	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28586910	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28588872	0.80[AMR][1000 genomes]
rs28630797	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs3864130	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934459	0.82[AMR][1000 genomes]
rs4463020	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs4505760	0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71602496	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	1.00[CHD][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs9991613	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9992641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv10412	chr4:649291-651178	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28742899	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs28742899	POLN	cis	parietal	SCAN
rs28742899	ZNF141	cis	cerebellum	SCAN
rs28742899	RP11-1191J2.2	cis	lung	GTEx
rs28742899	MYOZ3	trans	parietal	SCAN
rs28742899	RP11-1191J2.2	cis	Thyroid	GTEx
rs28742899	ZNF721	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:645800-656800	Weak transcription	Gastric	stomach
8	chr4:646800-650600	Enhancers	Brain Angular Gyrus	brain
9	chr4:647000-650000	Enhancers	Brain Anterior Caudate	brain
10	chr4:647200-651200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:648400-650200	Enhancers	Brain Substantia Nigra	brain
12	chr4:648400-657000	Weak transcription	Right Ventricle	heart
13	chr4:648600-650000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr4:648600-650600	Enhancers	Spleen	Spleen
15	chr4:648800-650000	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr4:648800-650800	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:648800-653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:649000-651000	Enhancers	Brain Hippocampus Middle	brain
19	chr4:649000-652800	Weak transcription	Brain Germinal Matrix	brain
20	chr4:649200-652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:649200-653000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:649400-649800	ZNF genes & repeats	Pancreas	Pancrea
23	chr4:649400-650000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:649600-650000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:649600-650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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