Variant report

Variant	rs9972613
Chromosome Location	chr15:78473549-78473550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:78473341-78473634	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:78473420-78473570	GM12870	blood:	n/a	n/a
3	SMC3	chr15:78473409-78473598	HepG2	liver:	n/a	n/a
4	CTCF	chr15:78473440-78473590	GM12874	blood:	n/a	n/a
5	CTCF	chr15:78473420-78473570	HEK293	kidney:	n/a	n/a
6	CTCF	chr15:78473400-78473550	A549	lung:	n/a	n/a
7	CTCF	chr15:78473400-78473550	HCPEpiC	choroid plexus:	n/a	n/a
8	CTCF	chr15:78473400-78473550	GM12873	blood:	n/a	n/a
9	CTCF	chr15:78473440-78473590	GM12866	blood:	n/a	n/a
10	CTCF	chr15:78473520-78473670	AG04450	lung:	n/a	n/a
11	CTCF	chr15:78473460-78473610	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr15:78473420-78473570	GM12875	blood:	n/a	n/a
13	CTCF	chr15:78473420-78473570	GM12871	blood:	n/a	n/a
14	CTCF	chr15:78473440-78473590	GM12869	blood:	n/a	n/a
15	CTCF	chr15:78473400-78473550	AG04449	skin:	n/a	n/a
16	CTCF	chr15:78473440-78473590	AG10803	skin:	n/a	n/a
17	CTCF	chr15:78473400-78473550	K562	blood:	n/a	n/a
18	CTCF	chr15:78473400-78473550	HPF	lung:	n/a	n/a
19	CTCF	chr15:78473400-78473550	BE2_C	brain:	n/a	n/a
20	CTCF	chr15:78473440-78473590	HCM	heart:	n/a	n/a
21	CTCF	chr15:78473520-78473670	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr15:78473420-78473570	GM12874	blood:	n/a	n/a
23	CTCF	chr15:78473400-78473550	HRE	kidney:	n/a	n/a
24	CTCF	chr15:78473440-78473590	K562	blood:	n/a	n/a
25	CTCF	chr15:78473203-78473758	A549	lung:	n/a	n/a
26	CTCF	chr15:78473420-78473570	BE2_C	brain:	n/a	n/a
27	CTCF	chr15:78473400-78473550	GM12878	blood:	n/a	n/a
28	CTCF	chr15:78473400-78473550	GM12867	blood:	n/a	n/a
29	CTCF	chr15:78473400-78473550	GM12864	blood:	n/a	n/a
30	CTCF	chr15:78473420-78473570	GM12864	blood:	n/a	n/a
31	CTCF	chr15:78473500-78473650	NHEK	skin:	n/a	n/a
32	CTCF	chr15:78473400-78473550	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr15:78473440-78473590	MCF-7	breast:	n/a	n/a
34	CTCF	chr15:78473420-78473570	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr15:78473420-78473570	GM12869	blood:	n/a	n/a
36	CTCF	chr15:78473400-78473550	GM12870	blood:	n/a	n/a
37	CTCF	chr15:78473500-78473650	HCT-116	colon:	n/a	n/a
38	CTCF	chr15:78473420-78473570	GM12866	blood:	n/a	n/a
39	CTCF	chr15:78473440-78473590	HFF-Myc	foreskin:	n/a	n/a
40	CTCF	chr15:78473400-78473550	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr15:78473440-78473590	HRPEpiC	eye:	n/a	n/a
42	RAD21	chr15:78473305-78473630	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr15:78473400-78473550	HEK293	kidney:	n/a	n/a
44	CTCF	chr15:78473440-78473590	AG09309	skin:	n/a	n/a
45	CTCF	chr15:78473440-78473590	GM12868	blood:	n/a	n/a
46	CTCF	chr15:78473420-78473570	GM12865	blood:	n/a	n/a
47	CTCF	chr15:78473480-78473630	BJ	skin:	n/a	n/a
48	CTCF	chr15:78473400-78473550	AG04450	lung:	n/a	n/a
49	CTCF	chr15:78473420-78473570	SAEC	small airway:	n/a	n/a
50	CTCF	chr15:78473400-78473550	HPAF	blood vessel:	n/a	n/a

No data

Variant related genes	Relation type
ACSBG1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11072738	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11855354	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903696	0.80[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915990	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982242	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304824	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495275	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7172176	0.81[ASN][1000 genomes]
rs8032618	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035724	0.88[MKK][hapmap]
rs9920103	0.82[CEU][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9972613	IDH3A	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78460200-78474200	Weak transcription	HepG2	liver
3	chr15:78464800-78475000	Weak transcription	HMEC	breast
4	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:78465400-78475200	Weak transcription	NHEK	skin
9	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
11	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
12	chr15:78470200-78477000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain
15	chr15:78470600-78477200	Weak transcription	Brain Anterior Caudate	brain
16	chr15:78470600-78486600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:78471200-78475800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:78472000-78473600	Enhancers	Spleen	Spleen
19	chr15:78472400-78473800	Enhancers	Thymus	Thymus
20	chr15:78472400-78475400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:78472800-78473600	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:78473200-78473800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr15:78473400-78473600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:78473400-78473600	Enhancers	Psoas Muscle	Psoas
25	chr15:78473400-78473600	Enhancers	Skeletal Muscle Female	skeletal muscle

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