Variant report

Variant	rs1496712
Chromosome Location	chr15:93198296-93198297
allele	A/G
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	chr15:93198249-93199577	H1-hESC	embryonic stem cell:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
2	ELF1	chr15:93198291-93199247	GM12878	blood:	n/a	chr15:93199043-93199052 chr15:93198982-93198991 chr15:93198983-93198995
3	MAX	chr15:93198271-93199489	A549	lung:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
4	HDAC2	chr15:93198295-93199446	MCF-7	breast:	n/a	chr15:93198329-93198343
5	RAD21	chr15:93198267-93199198	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:93198205-93199327	MCF-7	breast:	n/a	n/a
7	MAX	chr15:93198168-93198778	MCF-7	breast:	n/a	n/a
8	MYC	chr15:93198287-93199268	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
9	MXI1	chr15:93198282-93199977	SK-N-SH	brain:	n/a	chr15:93199093-93199102 chr15:93199095-93199104
10	MAZ	chr15:93197964-93198577	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr15:93198106-93199396	MCF-7	breast:	n/a	n/a
12	ZEB1	chr15:93198241-93198742	GM12878	blood:	n/a	chr15:93198446-93198457 chr15:93198460-93198469
13	E2F6	chr15:93198205-93199607	H1-hESC	embryonic stem cell:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
14	REST	chr15:93197985-93199487	H1-neurons	neurons:	n/a	chr15:93198949-93198969 chr15:93198448-93198461
15	MAX	chr15:93198203-93199479	ECC-1	luminal epithelium:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
16	MAX	chr15:93198284-93199459	ECC-1	luminal epithelium:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
17	HA-E2F1	chr15:93198231-93199645	MCF-7	breast:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
18	TAF1	chr15:93198288-93199195	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr15:93198228-93199447	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107

No.	Distal block	Cell Line	Cell type
1	chr15:93145840..93149737-chr15:93196292..93199149,3	MCF-7	breast:
2	chr15:93197537..93199243-chr15:93427702..93429402,2	MCF-7	breast:
3	chr15:93197891..93200562-chr3:14219402..14221003,2	MCF-7	breast:
4	chr15:93187167..93190385-chr15:93197959..93201879,3	K562	blood:
5	chr15:93196488..93198404-chr17:67442282..67443797,2	MCF-7	breast:

Variant related genes	Relation type
FAM174B	TF binding region
ENSG00000185442	Chromatin interaction
ENSG00000170860	Chromatin interaction
ENSG00000271763	Chromatin interaction
ENSG00000272888	Chromatin interaction
ENSG00000154767	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12443091	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254142	0.91[EUR][1000 genomes]
rs2453901	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.89[EUR][1000 genomes]
rs285755	0.90[EUR][1000 genomes]
rs285757	0.90[EUR][1000 genomes]
rs285758	0.90[EUR][1000 genomes]
rs285766	0.82[EUR][1000 genomes]
rs285772	0.92[EUR][1000 genomes]
rs366789	0.84[EUR][1000 genomes]
rs373481	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496969	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3374130	chr15:93197573-93200121	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1496712	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:93193800-93199000	Enhancers	Fetal Heart	heart
3	chr15:93194400-93198400	Weak transcription	Brain Anterior Caudate	brain
4	chr15:93194600-93198400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:93195800-93198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:93196600-93199200	Enhancers	Fetal Brain Male	brain
8	chr15:93196800-93198400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:93197000-93198400	Enhancers	Esophagus	oesophagus
10	chr15:93197000-93199600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:93197200-93198400	Enhancers	Brain Substantia Nigra	brain
12	chr15:93197200-93198400	Weak transcription	Placenta	Placenta
13	chr15:93197200-93198400	Weak transcription	Spleen	Spleen
14	chr15:93197200-93199000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:93197200-93199400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:93197200-93199400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr15:93197200-93199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:93197400-93198400	Enhancers	Primary hematopoietic stem cells	blood
19	chr15:93197400-93198400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr15:93197400-93198400	Flanking Active TSS	GM12878-XiMat	blood
21	chr15:93197400-93199400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr15:93197400-93199600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr15:93197600-93198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:93197600-93198400	Flanking Active TSS	Fetal Stomach	stomach
25	chr15:93197600-93198400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr15:93197600-93198600	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr15:93197600-93198800	Active TSS	Gastric	stomach
28	chr15:93197600-93199200	Active TSS	HSMM	muscle
29	chr15:93197600-93199400	Active TSS	Pancreas	Pancrea
30	chr15:93197800-93198400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr15:93197800-93198400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr15:93197800-93198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:93197800-93198400	Weak transcription	Left Ventricle	heart
34	chr15:93197800-93199000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr15:93197800-93199000	Active TSS	Small Intestine	intestine
36	chr15:93197800-93199200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr15:93197800-93199200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr15:93197800-93199200	Active TSS	Brain Cingulate Gyrus	brain
39	chr15:93197800-93199200	Active TSS	Brain Hippocampus Middle	brain
40	chr15:93197800-93199200	Active TSS	Fetal Intestine Small	intestine
41	chr15:93197800-93199200	Active TSS	Stomach Mucosa	stomach
42	chr15:93197800-93199400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr15:93197800-93199400	Active TSS	Ovary	ovary
44	chr15:93197800-93199600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr15:93198000-93198400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr15:93198000-93198400	Enhancers	Liver	Liver
47	chr15:93198000-93198400	Active TSS	Colonic Mucosa	Colon
48	chr15:93198000-93198400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr15:93198000-93198400	Weak transcription	Fetal Kidney	kidney
50	chr15:93198000-93198400	Active TSS	Right Atrium	heart

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