Variant report

Variant	rs3794494
Chromosome Location	chr15:59464896-59464897
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	RAD21	chr15:59464720-59465058	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr15:59464677-59464986	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr15:59464820-59464970	HFF	foreskin:	n/a	n/a
4	CTCF	chr15:59464860-59465010	HPF	lung:	n/a	n/a
5	CTCF	chr15:59464760-59464910	GM12872	blood:	n/a	chr15:59464819-59464827
6	CTCF	chr15:59464820-59464970	GM12868	blood:	n/a	n/a
7	RAD21	chr15:59464765-59465072	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr15:59464860-59465010	HVMF	connective:	n/a	n/a
9	CTCF	chr15:59464800-59464950	HMEC	breast:	n/a	chr15:59464819-59464827
10	CTCF	chr15:59464780-59464930	Hela-S3	cervix:	n/a	chr15:59464819-59464827
11	CTCF	chr15:59464760-59464910	HPF	lung:	n/a	chr15:59464819-59464827
12	CTCF	chr15:59464800-59464950	NHLF	lung:	n/a	chr15:59464819-59464827
13	CTCF	chr15:59464800-59464950	HCT-116	colon:	n/a	chr15:59464819-59464827
14	CTCF	chr15:59464760-59464910	GM12871	blood:	n/a	chr15:59464819-59464827
15	CTCF	chr15:59464880-59465030	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr15:59464780-59464930	HEEpiC	esophagus:	n/a	chr15:59464819-59464827
17	CTCF	chr15:59464780-59464930	HBMEC	blood vessel:	n/a	chr15:59464819-59464827
18	CTCF	chr15:59464780-59464930	HRE	kidney:	n/a	chr15:59464819-59464827
19	RAD21	chr15:59464756-59464956	HepG2	liver:	n/a	n/a
20	CTCF	chr15:59464840-59464990	GM12867	blood:	n/a	n/a
21	CTCF	chr15:59464780-59464930	RPTEC	kidney:	n/a	chr15:59464819-59464827
22	CTCF	chr15:59464760-59464910	HRE	kidney:	n/a	chr15:59464819-59464827
23	CTCF	chr15:59464800-59464950	AG10803	skin:	n/a	chr15:59464819-59464827
24	CTCF	chr15:59464860-59465010	AG04450	lung:	n/a	n/a
25	POLR2A	chr15:59464680-59465096	A549	lung:	n/a	n/a
26	CTCF	chr15:59464880-59465030	A549	lung:	n/a	n/a
27	SMC3	chr15:59464724-59464974	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr15:59464860-59465010	MCF-7	breast:	n/a	n/a
29	CTCF	chr15:59464797-59464969	Hela-S3	cervix:	n/a	chr15:59464819-59464827
30	CTCF	chr15:59464760-59464910	HMEC	breast:	n/a	chr15:59464819-59464827
31	CTCF	chr15:59464760-59464910	GM12864	blood:	n/a	chr15:59464819-59464827
32	CTCF	chr15:59464820-59464970	GM12867	blood:	n/a	n/a
33	CTCF	chr15:59464820-59464970	HPAF	blood vessel:	n/a	n/a
34	CTCF	chr15:59464840-59464990	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr15:59464800-59464950	HMF	breast:	n/a	chr15:59464819-59464827
36	CTCF	chr15:59464760-59464910	HA-sp	spinal cord:	n/a	chr15:59464819-59464827
37	CTCF	chr15:59464800-59464950	HCFaa	heart:	n/a	chr15:59464819-59464827
38	CTCF	chr15:59464815-59464910	MCF-7	breast:	n/a	chr15:59464819-59464827
39	CTCF	chr15:59464860-59465010	HCPEpiC	choroid plexus:	n/a	n/a
40	CTCF	chr15:59464820-59464970	Caco-2	colon:	n/a	n/a
41	CTCF	chr15:59464815-59464931	HepG2	liver:	n/a	chr15:59464819-59464827
42	CTCF	chr15:59464800-59464950	AG04449	skin:	n/a	chr15:59464819-59464827
43	CTCF	chr15:59464760-59464910	AG04450	lung:	n/a	chr15:59464819-59464827
44	CTCF	chr15:59464811-59464948	HUVEC	blood vessel:	n/a	chr15:59464819-59464827
45	CTCF	chr15:59464800-59464950	MCF-7	breast:	n/a	chr15:59464819-59464827
46	CTCF	chr15:59464780-59464930	HAc	cerebellar:	n/a	chr15:59464819-59464827
47	RAD21	chr15:59464728-59464960	SK-N-SH_RA	brain:	n/a	n/a
48	RAD21	chr15:59464672-59465115	ECC-1	luminal epithelium:	n/a	n/a
49	RAD21	chr15:59464640-59465070	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr15:59464807-59465027	GM12878	blood:	n/a	chr15:59464819-59464827

Variant related genes	Relation type
MIR2116	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10519001	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851644	0.82[CEU][hapmap]
rs11071412	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630106	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11631348	0.80[EUR][1000 genomes]
rs11632420	0.80[EUR][1000 genomes]
rs12898967	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12903377	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906742	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12916830	0.81[AMR][1000 genomes]
rs17269566	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306787	0.96[CEU][hapmap]
rs2306788	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306789	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794499	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794500	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775124	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775130	0.95[CEU][hapmap]
rs56108450	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58948844	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7169503	0.92[CEU][hapmap]
rs901481	0.90[ASN][1000 genomes]
rs9788755	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3794494	GCOM1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59431800-59467200	Weak transcription	Fetal Brain Female	brain
2	chr15:59432000-59465600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59434200-59467000	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
5	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
6	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
7	chr15:59445800-59467000	Weak transcription	Fetal Heart	heart
8	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
11	chr15:59451800-59466000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:59453400-59467200	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:59453800-59470000	Weak transcription	Right Ventricle	heart
14	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:59455200-59467200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:59458000-59470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr15:59459200-59466800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:59459400-59467000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:59460600-59465800	Strong transcription	GM12878-XiMat	blood
22	chr15:59460800-59466200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:59461000-59474800	Strong transcription	Liver	Liver
24	chr15:59461200-59466200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:59461200-59467000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:59461400-59466800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:59461600-59466400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:59461800-59467200	Strong transcription	Hela-S3	cervix
29	chr15:59462000-59465000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:59462000-59466800	Strong transcription	Fetal Intestine Small	intestine
31	chr15:59462000-59467000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:59462000-59467200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr15:59462400-59465400	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:59462400-59465400	Strong transcription	Fetal Stomach	stomach
35	chr15:59462400-59467200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:59462600-59466800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr15:59462800-59466200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:59462800-59466800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:59462800-59467000	Weak transcription	Right Atrium	heart
40	chr15:59463000-59466000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:59463000-59466600	Weak transcription	Stomach Mucosa	stomach
42	chr15:59463000-59466800	Weak transcription	Adipose Nuclei	Adipose
43	chr15:59463000-59467000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:59463200-59465000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr15:59463200-59465400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:59463200-59465800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:59463200-59466600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr15:59463200-59466800	Weak transcription	Brain Anterior Caudate	brain
49	chr15:59463200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:59463200-59467000	Strong transcription	A549	lung

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