Variant report

Variant	rs4415117
Chromosome Location	chr5:1594995-1594996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:127)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:127 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr5:1594482-1595044	HepG2	liver:	n/a	n/a
2	CTCF	chr5:1594294-1595230	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:1594156-1595074	GM15510	blood:	n/a	n/a
4	YY1	chr5:1594321-1595057	GM12878	blood:	n/a	n/a
5	ZEB1	chr5:1594798-1595058	GM12878	blood:	n/a	n/a
6	CTCF	chr5:1594319-1595067	K562	blood:	n/a	n/a
7	POLR2A	chr5:1594123-1595053	MCF-7	breast:	n/a	n/a
8	MAX	chr5:1594530-1595045	A549	lung:	n/a	n/a
9	MAX	chr5:1594471-1595086	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr5:1594245-1595060	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:1593846-1595062	GM12878	blood:	n/a	n/a
12	NRF1	chr5:1594363-1595222	SK-N-SH	brain:	n/a	chr5:1594676-1594687
13	MAX	chr5:1594378-1595000	SK-N-SH	brain:	n/a	n/a
14	ZBTB7A	chr5:1594464-1595105	ECC-1	luminal epithelium:	n/a	n/a
15	HA-E2F1	chr5:1594267-1595315	MCF-7	breast:	n/a	chr5:1594936-1594948
16	RCOR1	chr5:1594429-1595008	GM12878	blood:	n/a	n/a
17	MAX	chr5:1594543-1595048	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr5:1594148-1595076	GM18505	blood:	n/a	n/a
19	YY1	chr5:1594310-1594997	GM12878	blood:	n/a	n/a
20	HEY1	chr5:1594432-1595021	HepG2	liver:	n/a	n/a
21	ELF1	chr5:1594668-1595202	K562	blood:	n/a	chr5:1594929-1594938 chr5:1594930-1594942
22	POLR2A	chr5:1594337-1595064	HepG2	liver:	n/a	n/a
23	YY1	chr5:1594261-1595059	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:1594346-1595052	GM19193	blood:	n/a	n/a
25	E2F6	chr5:1594413-1595007	K562	blood:	n/a	chr5:1594936-1594948
26	POLR2A	chr5:1593574-1595153	HepG2	liver:	n/a	n/a
27	MAX	chr5:1594405-1595179	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr5:1594366-1595002	Hela-S3	cervix:	n/a	n/a
29	TBP	chr5:1594494-1595217	K562	blood:	n/a	n/a
30	POLR2A	chr5:1594059-1595070	ECC-1	luminal epithelium:	n/a	n/a
31	SMARCB1	chr5:1594443-1595036	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr5:1594310-1595025	A549	lung:	n/a	n/a
33	TAF1	chr5:1594413-1595183	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr5:1594356-1595017	HepG2	liver:	n/a	n/a
35	SP1	chr5:1594962-1595258	GM12878	blood:	n/a	n/a
36	CTCF	chr5:1594548-1595029	MCF-7	breast:	n/a	n/a
37	E2F6	chr5:1594406-1595033	K562	blood:	n/a	chr5:1594936-1594948
38	MAX	chr5:1594391-1595009	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr5:1594339-1595062	K562	blood:	n/a	n/a
40	POLR2A	chr5:1594355-1595043	GM18526	blood:	n/a	n/a
41	POLR2A	chr5:1593680-1595156	GM12892	blood:	n/a	n/a
42	HDAC2	chr5:1594428-1595089	HepG2	liver:	n/a	n/a
43	POU2F2	chr5:1594288-1595318	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:1594391-1595040	GM10847	blood:	n/a	n/a
45	HEY1	chr5:1593757-1595375	HepG2	liver:	n/a	n/a
46	POLR2A	chr5:1594087-1595040	MCF-7	breast:	n/a	n/a
47	MAX	chr5:1594466-1595029	MCF-7	breast:	n/a	n/a
48	GTF3C2	chr5:1594437-1595197	K562	blood:	n/a	n/a
49	POLR2A	chr5:1594323-1595087	Hela-S3	cervix:	n/a	n/a
50	YY1	chr5:1594170-1595094	HepG2	liver:	n/a	chr5:1594250-1594259

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1521816..1527528-chr5:1592860..1598605,11	MCF-7	breast:
2	chr5:1514406..1516208-chr5:1594947..1596689,2	MCF-7	breast:
3	chr5:1523398..1525514-chr5:1593049..1596124,4	MCF-7	breast:

No data

Variant related genes	Relation type
SDHAP3	TF binding region
ENSG00000248126	TF binding region
ENSG00000153395	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10512659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11133831	1.00[ASN][1000 genomes]
rs11948870	1.00[ASN][1000 genomes]
rs11951409	1.00[ASN][1000 genomes]
rs11951807	1.00[ASN][1000 genomes]
rs11951980	1.00[ASN][1000 genomes]
rs11952238	1.00[ASN][1000 genomes]
rs11953233	1.00[ASN][1000 genomes]
rs11954077	1.00[ASN][1000 genomes]
rs11955967	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957991	1.00[ASN][1000 genomes]
rs11958097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17530842	1.00[CHB][hapmap]
rs17596634	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2883372	1.00[ASN][1000 genomes]
rs4246747	0.81[AFR][1000 genomes]
rs55864560	1.00[ASN][1000 genomes]
rs55867519	1.00[ASN][1000 genomes]
rs55957581	1.00[ASN][1000 genomes]
rs56185279	1.00[ASN][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	1.00[ASN][1000 genomes]
rs59610035	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59656356	1.00[ASN][1000 genomes]
rs59806631	1.00[ASN][1000 genomes]
rs61340395	1.00[ASN][1000 genomes]
rs6867199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6869310	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6870117	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6871261	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6872202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884318	1.00[ASN][1000 genomes]
rs6888170	1.00[ASN][1000 genomes]
rs6888910	1.00[ASN][1000 genomes]
rs6889629	1.00[ASN][1000 genomes]
rs6889684	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717589	1.00[ASN][1000 genomes]
rs72717593	1.00[ASN][1000 genomes]
rs72717595	1.00[ASN][1000 genomes]
rs72717596	1.00[ASN][1000 genomes]
rs72717598	1.00[ASN][1000 genomes]
rs72717600	1.00[ASN][1000 genomes]
rs73732121	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732122	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732124	1.00[ASN][1000 genomes]
rs73732134	1.00[ASN][1000 genomes]
rs7708447	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716004	1.00[ASN][1000 genomes]
rs7725592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728463	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728632	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729323	1.00[ASN][1000 genomes]
rs7732756	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736524	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7736669	1.00[ASN][1000 genomes]
rs7737033	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7737331	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880471	chr5:1466813-1598468	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
5	nsv881644	chr5:1478021-1597272	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
7	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
9	nsv881574	chr5:1537141-1598468	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv881282	chr5:1549771-1597272	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4415117	SDHAP3	cis	Esophagus Mucosa	GTEx
rs4415117	SDHAP3	cis	Whole Blood	GTEx
rs4415117	SDHAP3	cis	Esophagus Muscularis	GTEx
rs4415117	SDHAP3	cis	Nerve Tibial	GTEx
rs4415117	SDHAP3	cis	Thyroid	GTEx
rs4415117	SDHAP3	cis	Artery Tibial	GTEx
rs4415117	RP11-43F13.1	cis	Whole Blood	GTEx
rs4415117	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs4415117	CTD-2012J19.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1582400-1595000	Weak transcription	Fetal Heart	heart
2	chr5:1593200-1595000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:1593200-1595400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:1593400-1595000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:1593400-1595200	Active TSS	GM12878-XiMat	blood
6	chr5:1593400-1595400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:1593400-1595400	Active TSS	Brain Germinal Matrix	brain
8	chr5:1593600-1595200	Active TSS	HepG2	liver
9	chr5:1593600-1595400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:1593800-1595000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr5:1593800-1595000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:1593800-1595200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr5:1593800-1595200	Active TSS	Hela-S3	cervix
14	chr5:1593800-1595400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr5:1593800-1595400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:1593800-1595400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr5:1593800-1595400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:1593800-1595400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr5:1593800-1595400	Active TSS	Fetal Brain Female	brain
20	chr5:1594000-1595000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:1594000-1595000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:1594000-1595000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:1594000-1595000	Active TSS	Fetal Intestine Small	intestine
24	chr5:1594000-1595000	Active TSS	Rectal Smooth Muscle	rectum
25	chr5:1594000-1595200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:1594000-1595200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr5:1594000-1595200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:1594000-1595200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:1594000-1595200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:1594000-1595200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:1594000-1595200	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr5:1594000-1595200	Active TSS	Primary T cells from cord blood	blood
33	chr5:1594000-1595200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr5:1594000-1595200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr5:1594000-1595200	Active TSS	Brain Angular Gyrus	brain
36	chr5:1594000-1595200	Active TSS	Brain Anterior Caudate	brain
37	chr5:1594000-1595200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:1594000-1595200	Active TSS	Left Ventricle	heart
39	chr5:1594000-1595200	Active TSS	Right Atrium	heart
40	chr5:1594000-1595200	Active TSS	Right Ventricle	heart
41	chr5:1594000-1595200	Active TSS	Thymus	Thymus
42	chr5:1594000-1595200	Active TSS	HSMM	muscle
43	chr5:1594000-1595200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr5:1594000-1595200	Active TSS	NHLF	lung
45	chr5:1594000-1595400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:1594000-1595400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:1594000-1595400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr5:1594000-1595400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr5:1594000-1595400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:1594000-1595400	Active TSS	Colon Smooth Muscle	Colon

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