Variant report

Variant	rs324419
Chromosome Location	chr1:46871986-46871987
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	YY1	chr1:46871897-46872388	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr1:46871977-46872322	A549	lung:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
3	CTCF	chr1:46871985-46871994	Spleen_OC	spleen:	n/a	n/a
4	ESR1	chr1:46871644-46872000	ECC-1	luminal epithelium:	n/a	chr1:46871789-46871806
5	POLR2A	chr1:46871910-46872018	HepG2	liver:	n/a	n/a
6	CTCF	chr1:46871794-46872474	HCT-116	colon:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
7	CTCF	chr1:46871821-46872354	GM12892	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
8	CTCF	chr1:46871637-46872392	SK-N-SH	brain:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
9	RAD21	chr1:46871920-46872318	MCF-7	breast:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
10	YY1	chr1:46871953-46872356	K562	blood:	n/a	n/a
11	ZNF143	chr1:46871951-46872318	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr1:46871974-46872347	HepG2	liver:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
13	RAD21	chr1:46871822-46872306	HCT-116	colon:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
14	RAD21	chr1:46871986-46872272	GM12878	blood:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
15	CTCF	chr1:46871845-46872287	Gliobla	brain:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
16	CTCF	chr1:46871962-46872383	IMR90	lung:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
17	CTCF	chr1:46871980-46872130	HAc	cerebellar:	n/a	n/a
18	SMC3	chr1:46871671-46872388	SK-N-SH	brain:	n/a	chr1:46872185-46872199 chr1:46872185-46872192
19	SMC3	chr1:46871981-46872372	Hela-S3	cervix:	n/a	chr1:46872185-46872199 chr1:46872185-46872192
20	CTCF	chr1:46871948-46872285	HepG2	liver:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
21	CTCF	chr1:46871870-46872315	MCF-7	breast:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
22	RAD21	chr1:46871934-46872354	HepG2	liver:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
23	CTCF	chr1:46871973-46872343	K562	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
24	ESR1	chr1:46871584-46872070	ECC-1	luminal epithelium:	n/a	chr1:46871789-46871806
25	RAD21	chr1:46871924-46872437	H1-hESC	embryonic stem cell:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
26	ZNF384	chr1:46871859-46872936	K562	blood:	n/a	n/a
27	RAD21	chr1:46871896-46872322	A549	lung:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
28	POLR2A	chr1:46871865-46872060	MCF-7	breast:	n/a	n/a
29	FOXM1	chr1:46871939-46872312	GM12878	blood:	n/a	n/a
30	SIN3A	chr1:46871979-46872247	H1-hESC	embryonic stem cell:	n/a	n/a
31	HMGN3	chr1:46871739-46872157	K562	blood:	n/a	n/a
32	RAD21	chr1:46871898-46872281	ECC-1	luminal epithelium:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
33	RAD21	chr1:46871986-46872351	SK-N-SH_RA	brain:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
34	CTCF	chr1:46871802-46872373	A549	lung:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
35	CTCF	chr1:46871915-46872278	MCF-7	breast:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
36	CTCF	chr1:46871916-46872505	K562	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
37	CTCF	chr1:46871980-46872344	H1-hESC	embryonic stem cell:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
38	CTCF	chr1:46871882-46872380	GM12878	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
39	ZMIZ1	chr1:46871903-46872223	K562	blood:	n/a	n/a
40	RAD21	chr1:46871750-46872372	SK-N-SH	brain:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
41	CTCF	chr1:46871961-46872351	K562	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
42	CTCF	chr1:46871972-46872344	A549	lung:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
43	RAD21	chr1:46871916-46872441	HCT-116	colon:	n/a	chr1:46872185-46872199 chr1:46872184-46872203
44	RCOR1	chr1:46871846-46872230	K562	blood:	n/a	n/a
45	CTCF	chr1:46871818-46872333	GM19238	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
46	CTCF	chr1:46871981-46872392	K562	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
47	CTCF	chr1:46871768-46872320	GM12891	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200
48	MAZ	chr1:46871799-46872319	IMR90	lung:	n/a	n/a
49	RUNX3	chr1:46871979-46872232	GM12878	blood:	n/a	n/a
50	CTCF	chr1:46871813-46872358	GM19240	blood:	n/a	chr1:46872183-46872201 chr1:46872186-46872199 chr1:46872185-46872206 chr1:46872184-46872200

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46871688..46875401-chr1:47182655..47185240,3	K562	blood:
2	chr1:46871867..46872690-chr1:46942756..46943813,5	K562	blood:

Variant related genes	Relation type
FAAH	TF binding region
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs324416	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS 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	32 gene(s)	inside rSNPs	diseases
7	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs324419	FAAH	cis	cerebellum	SCAN
rs324419	C1orf228	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:46861200-46872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
4	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:46864000-46872400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:46865400-46876000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:46866200-46872000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:46866400-46872600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:46867800-46872400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:46867800-46872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:46867800-46872600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:46867800-46872600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:46867800-46877000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:46868000-46872000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:46868000-46876200	Weak transcription	Small Intestine	intestine
17	chr1:46868000-46884200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:46868200-46872000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:46868200-46872000	Weak transcription	Fetal Brain Female	brain
20	chr1:46868200-46872000	Weak transcription	Left Ventricle	heart
21	chr1:46868200-46872200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:46868200-46873200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:46868200-46873600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:46868200-46875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:46868200-46883800	Weak transcription	HepG2	liver
26	chr1:46868400-46872800	Weak transcription	NHEK	skin
27	chr1:46869000-46872200	Strong transcription	Thymus	Thymus
28	chr1:46869000-46882000	Strong transcription	Fetal Intestine Small	intestine
29	chr1:46870200-46872600	Genic enhancers	Colonic Mucosa	Colon
30	chr1:46870200-46874000	Enhancers	K562	blood
31	chr1:46870400-46873200	Genic enhancers	Brain Cingulate Gyrus	brain
32	chr1:46870600-46872000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:46870600-46872600	Enhancers	Brain Hippocampus Middle	brain
34	chr1:46870800-46872200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:46871000-46872000	Weak transcription	Brain Germinal Matrix	brain
36	chr1:46871000-46872800	Weak transcription	Liver	Liver
37	chr1:46871000-46873000	Enhancers	Brain Substantia Nigra	brain
38	chr1:46871000-46873600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:46871200-46872200	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:46871400-46872200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:46871400-46872200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:46871400-46872400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:46871400-46873400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:46871600-46872000	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:46871600-46872200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:46871600-46872200	Genic enhancers	Gastric	stomach
47	chr1:46871600-46872200	Enhancers	Ovary	ovary
48	chr1:46871600-46872400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:46871600-46872800	Enhancers	Right Ventricle	heart
50	chr1:46871600-46872800	Enhancers	Spleen	Spleen

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