Variant report

Variant	rs11584024
Chromosome Location	chr1:46656964-46656965
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	POLR2A	chr1:46656113-46657169	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr1:46656189-46657001	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr1:46656709-46657082	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46649532..46653630-chr1:46654229..46657626,5	K562	blood:
2	chr1:46641730..46644233-chr1:46656558..46658079,2	K562	blood:
3	chr1:46655055..46657089-chr1:46660315..46664109,3	K562	blood:
4	chr1:46655107..46657515-chr1:46657628..46660092,2	K562	blood:

Variant related genes	Relation type
POMGNT1	TF binding region
ENSG00000117472	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11584436	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12047449	0.83[EUR][1000 genomes]
rs2234270	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61784560	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61784561	0.82[AMR][1000 genomes];0.98[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	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv527878	chr1:46649046-46660295	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv822520	chr1:46650486-46661701	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11584024	CCDC24	cis	cerebellum	SCAN
rs11584024	FAAH	cis	cerebellum	SCAN
rs11584024	C1orf228	cis	parietal	SCAN
rs11584024	KDM4A	cis	cerebellum	SCAN
rs11584024	CYP4Z1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46645200-46657800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:46645600-46658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:46645800-46663200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:46646000-46657600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:46648400-46657800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:46649200-46657600	Weak transcription	Fetal Lung	lung
7	chr1:46649400-46662400	Strong transcription	Fetal Stomach	stomach
8	chr1:46649800-46659800	Weak transcription	Fetal Heart	heart
9	chr1:46649800-46661400	Weak transcription	Psoas Muscle	Psoas
10	chr1:46649800-46663000	Weak transcription	HUVEC	blood vessel
11	chr1:46650200-46657200	Genic enhancers	HMEC	breast
12	chr1:46650400-46657400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:46650400-46662600	Weak transcription	Right Atrium	heart
14	chr1:46650600-46657200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:46650800-46662200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:46650800-46662600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:46651000-46662400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:46651000-46662600	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:46651200-46662800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:46651200-46663000	Strong transcription	NHLF	lung
21	chr1:46651600-46662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:46652000-46663200	Weak transcription	Fetal Kidney	kidney
23	chr1:46652600-46662800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:46652800-46657000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:46652800-46658200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:46652800-46659800	Strong transcription	Colon Smooth Muscle	Colon
27	chr1:46652800-46660000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:46652800-46660000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:46652800-46660200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:46652800-46660400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:46652800-46660400	Strong transcription	Brain Germinal Matrix	brain
32	chr1:46652800-46660400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:46652800-46661600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:46652800-46661800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:46652800-46662200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr1:46652800-46662400	Strong transcription	Primary T cells from cord blood	blood
37	chr1:46652800-46662400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:46652800-46662400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:46652800-46662800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:46652800-46662800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:46653000-46658600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:46653000-46659600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:46653000-46659800	Strong transcription	Brain Anterior Caudate	brain
44	chr1:46653000-46660600	Strong transcription	Brain Hippocampus Middle	brain
45	chr1:46653000-46662200	Strong transcription	Brain Angular Gyrus	brain
46	chr1:46653000-46662200	Strong transcription	Dnd41	blood
47	chr1:46653000-46662400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:46653000-46662400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:46653000-46662400	Strong transcription	Fetal Brain Female	brain
50	chr1:46653000-46662400	Strong transcription	Stomach Smooth Muscle	stomach

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