Variant report

Variant	rs8028374
Chromosome Location	chr15:99794174-99794175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr15:99793701-99794365	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr15:99793683-99794383	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr15:99794080-99794230	AG10803	skin:	n/a	n/a
4	MAX	chr15:99793814-99794258	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr15:99794160-99794310	HCFaa	heart:	n/a	n/a
6	RCOR1	chr15:99793849-99794177	K562	blood:	n/a	n/a
7	EP300	chr15:99793783-99794272	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr15:99794040-99794190	HCPEpiC	choroid plexus:	n/a	n/a
9	FOS	chr15:99793824-99794290	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr15:99793743-99794330	SK-N-SH	brain:	n/a	n/a
11	RUNX3	chr15:99793749-99794239	GM12878	blood:	n/a	n/a
12	CTCF	chr15:99794140-99794290	HMF	breast:	n/a	n/a
13	CTCF	chr15:99794080-99794230	HPF	lung:	n/a	n/a
14	TCF12	chr15:99793581-99794455	SK-N-SH	brain:	n/a	n/a
15	NFIC	chr15:99793538-99794396	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr15:99793837-99794237	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr15:99793514-99794557	SK-N-SH	brain:	n/a	n/a
18	JUND	chr15:99793668-99794448	SK-N-SH	brain:	n/a	n/a
19	EP300	chr15:99793783-99794175	SK-N-SH_RA	brain:	n/a	n/a
20	GATA3	chr15:99793567-99794521	SK-N-SH	brain:	n/a	n/a
21	SMC3	chr15:99794046-99794221	HepG2	liver:	n/a	n/a
22	CTCF	chr15:99794080-99794230	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr15:99794060-99794210	AG04449	skin:	n/a	n/a
24	CTCF	chr15:99794100-99794250	HPAF	blood vessel:	n/a	n/a
25	PBX3	chr15:99793702-99794469	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr15:99794080-99794230	HCM	heart:	n/a	n/a
27	CTCF	chr15:99794172-99794185	K562	blood:	n/a	n/a
28	CTCF	chr15:99794100-99794250	A549	lung:	n/a	n/a
29	CTCF	chr15:99794080-99794230	HMF	breast:	n/a	n/a
30	EP300	chr15:99793610-99794309	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr15:99794080-99794230	AG04449	skin:	n/a	n/a
32	TEAD4	chr15:99793702-99794397	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr15:99794120-99794270	MCF-7	breast:	n/a	n/a
34	CTCF	chr15:99793980-99794210	HPAF	blood vessel:	n/a	n/a
35	JUND	chr15:99793676-99794372	SK-N-SH	brain:	n/a	n/a
36	TCF12	chr15:99793575-99794354	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr15:99793764-99794285	SK-N-SH	brain:	n/a	n/a
38	GATA2	chr15:99793911-99794218	SH-SY5Y	brain:	n/a	n/a
39	CTCF	chr15:99794080-99794230	HBMEC	blood vessel:	n/a	n/a
40	IKZF1	chr15:99793742-99794483	GM12878	blood:	n/a	n/a
41	NFIC	chr15:99793645-99794357	SK-N-SH	brain:	n/a	n/a
42	GATA2	chr15:99793815-99794231	HUVEC	blood vessel:	n/a	n/a
43	CTCF	chr15:99794060-99794210	AoAF	blood vessel:	n/a	n/a
44	YY1	chr15:99793774-99794322	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr15:99794040-99794190	AoAF	blood vessel:	n/a	n/a

No data

Variant related genes	Relation type
TTC23	TF binding region
ENSG00000264771	TF binding region
HSP90B2P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10152456	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10152794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591132	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593449	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1567418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084900	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2902154	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55909409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56315393	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56341787	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56364603	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62023767	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62025697	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7170360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174431	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs7175165	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178124	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs735823	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs8025136	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029886	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031175	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs8042439	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8043311	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
10	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking 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	31 gene(s)	inside rSNPs	diseases
11	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
15	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
18	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8028374	SYNM	cis	parietal	SCAN
rs8028374	SYNM	cis	cerebellum	SCAN
rs8028374	TTC23	cis	cerebellum	SCAN
rs8028374	TTC23	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792200-99802800	Weak transcription	Esophagus	oesophagus
2	chr15:99792200-99807400	Weak transcription	Ovary	ovary
3	chr15:99792200-99846400	Weak transcription	Lung	lung
4	chr15:99792400-99804200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:99792600-99794200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr15:99792600-99794200	Enhancers	Small Intestine	intestine
7	chr15:99792600-99795000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:99792600-99832200	Weak transcription	Aorta	Aorta
9	chr15:99792800-99794200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:99792800-99794200	Enhancers	Fetal Thymus	thymus
11	chr15:99792800-99794200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:99792800-99794200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr15:99792800-99794400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:99792800-99794400	Enhancers	Primary B cells from cord blood	blood
15	chr15:99792800-99794400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:99792800-99794600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:99792800-99794800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:99792800-99796400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:99792800-99796400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:99792800-99798400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:99792800-99801600	Weak transcription	Fetal Stomach	stomach
22	chr15:99792800-99802800	Weak transcription	A549	lung
23	chr15:99792800-99804200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:99792800-99804600	Weak transcription	Placenta	Placenta
25	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
26	chr15:99793000-99794200	Enhancers	Primary T cells from cord blood	blood
27	chr15:99793000-99794200	Enhancers	Primary hematopoietic stem cells	blood
28	chr15:99793000-99794200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr15:99793000-99794200	Enhancers	Fetal Intestine Large	intestine
30	chr15:99793000-99794200	Enhancers	Fetal Intestine Small	intestine
31	chr15:99793000-99794200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr15:99793000-99794400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:99793000-99794400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr15:99793000-99794400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:99793000-99794400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:99793000-99794400	Enhancers	HMEC	breast
37	chr15:99793000-99794800	Enhancers	Dnd41	blood
38	chr15:99793000-99795000	Enhancers	HepG2	liver
39	chr15:99793000-99796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:99793000-99797800	Weak transcription	Fetal Lung	lung
41	chr15:99793000-99799000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:99793000-99799400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:99793000-99803200	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:99793000-99804200	Weak transcription	Fetal Heart	heart
45	chr15:99793000-99804400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:99793000-99804600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:99793000-99805400	Weak transcription	Fetal Brain Female	brain
48	chr15:99793000-99823800	Weak transcription	Fetal Brain Male	brain
49	chr15:99793000-99838000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:99793000-99850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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