Variant report

Variant	rs409200
Chromosome Location	chr15:93199453-93199454
allele	G/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	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	TCF12	chr15:93198781-93199512	A549	lung:	n/a	n/a
3	TCF7L2	chr15:93199060-93199495	PANC-1	pancreas:	n/a	n/a
4	MAX	chr15:93198271-93199489	A549	lung:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
5	MAX	chr15:93198792-93199533	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
6	RCOR1	chr15:93198933-93199509	GM12878	blood:	n/a	n/a
7	MTA3	chr15:93198825-93199667	GM12878	blood:	n/a	n/a
8	MXI1	chr15:93198282-93199977	SK-N-SH	brain:	n/a	chr15:93199093-93199102 chr15:93199095-93199104
9	E2F6	chr15:93198205-93199607	H1-hESC	embryonic stem cell:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
10	REST	chr15:93197985-93199487	H1-neurons	neurons:	n/a	chr15:93198949-93198969 chr15:93198448-93198461
11	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
12	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
13	HA-E2F1	chr15:93198231-93199645	MCF-7	breast:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
14	MAX	chr15:93198781-93199454	GM12878	blood:	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	chr15:93188112..93190385-chr15:93199041..93201879,2	K562	blood:
2	chr15:93199083..93200722-chr17:17739000..17741179,2	MCF-7	breast:
3	chr15:93197891..93200562-chr3:14219402..14221003,2	MCF-7	breast:
4	chr15:93187167..93190385-chr15:93197959..93201879,3	K562	blood:

Variant related genes	Relation type
FAM174B	TF binding region
ENSG00000185442	Chromatin interaction
ENSG00000170860	Chromatin interaction
ENSG00000154767	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs285762	0.96[EUR][1000 genomes]
rs435171	0.88[AMR][1000 genomes];1.00[EUR][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
rs409200	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:93197000-93199600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:93197200-93199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:93197400-93199600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr15:93197800-93199600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr15:93198000-93199600	Active TSS	Rectal Smooth Muscle	rectum
7	chr15:93198200-93199600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:93198800-93199600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:93199000-93199600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:93199000-93199600	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr15:93199000-93199600	Flanking Active TSS	Fetal Heart	heart
12	chr15:93199000-93199600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr15:93199000-93199600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr15:93199000-93199600	Flanking Active TSS	GM12878-XiMat	blood
15	chr15:93199000-93200000	Enhancers	Placenta	Placenta
16	chr15:93199200-93199600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:93199200-93199600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
18	chr15:93199200-93199600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr15:93199200-93199600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr15:93199200-93199600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr15:93199200-93199600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:93199200-93199600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr15:93199200-93199600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr15:93199200-93199600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
25	chr15:93199200-93199600	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr15:93199200-93199600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr15:93199200-93199600	Flanking Active TSS	Fetal Brain Male	brain
28	chr15:93199200-93199600	Flanking Active TSS	Fetal Brain Female	brain
29	chr15:93199200-93199600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
30	chr15:93199200-93199600	Enhancers	Left Ventricle	heart
31	chr15:93199200-93199600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
32	chr15:93199200-93199600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr15:93199200-93199800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:93199200-93199800	Enhancers	Lung	lung
35	chr15:93199200-93199800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:93199200-93200000	Enhancers	Stomach Mucosa	stomach
37	chr15:93199200-93200600	Enhancers	Gastric	stomach
38	chr15:93199200-93201000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:93199400-93199600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
40	chr15:93199400-93199600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr15:93199400-93199600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:93199400-93199600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr15:93199400-93199600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:93199400-93199600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr15:93199400-93199600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
46	chr15:93199400-93199600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
47	chr15:93199400-93199600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
48	chr15:93199400-93199600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
49	chr15:93199400-93199600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:93199400-93199600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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