Variant report

Variant	rs4981504
Chromosome Location	chr14:24791136-24791137
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	TEAD4	chr14:24790826-24791232	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
2	chr14:24700462..24703235-chr14:24790000..24792111,3	MCF-7	breast:
3	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
4	chr14:24790689..24792926-chr14:24801432..24803084,2	MCF-7	breast:

Variant related genes	Relation type
ADCY4	TF binding region
ENSG00000100445	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000255526	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11158632	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158634	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158635	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131941	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886362	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144494	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180196	0.90[GIH][hapmap]
rs2224122	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224123	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2281472	0.80[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2516564	0.85[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748543	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181384	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280164	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366641	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374085	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981503	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901500	chr14:24765622-24793762	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
4	nsv901501	chr14:24771285-24793762	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
5	nsv564059	chr14:24776401-24796813	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv564060	chr14:24776401-24809795	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4981504	LTB4R	cis	Thyroid	GTEx
rs4981504	LRRC16B	cis	parietal	SCAN
rs4981504	EDDM3A	cis	parietal	SCAN
rs4981504	NGDN	cis	parietal	SCAN
rs4981504	RABGGTA	cis	multi-tissue	Pritchard
rs4981504	LTB4R	cis	lung	GTEx
rs4981504	NDRG2	cis	parietal	SCAN
rs4981504	DHRS1	cis	cerebellum	SCAN
rs4981504	TGM1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24784600-24796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr14:24784800-24796600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr14:24786200-24801600	Weak transcription	Left Ventricle	heart
4	chr14:24786400-24792200	Weak transcription	Esophagus	oesophagus
5	chr14:24787000-24801200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:24787200-24796400	Weak transcription	Osteobl	bone
7	chr14:24787400-24791400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:24787800-24793600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr14:24788000-24792000	Weak transcription	Right Ventricle	heart
10	chr14:24788400-24801000	Weak transcription	Gastric	stomach
11	chr14:24788800-24791200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
12	chr14:24790400-24796400	Weak transcription	Colonic Mucosa	Colon
13	chr14:24790600-24794400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:24790800-24791200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:24790800-24791200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr14:24790800-24791400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:24790800-24791600	Strong transcription	Lung	lung
18	chr14:24790800-24791800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:24790800-24792200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr14:24790800-24792200	Bivalent Enhancer	HepG2	liver
21	chr14:24790800-24792600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:24790800-24792600	Enhancers	Placenta	Placenta
23	chr14:24790800-24793200	Strong transcription	Spleen	Spleen
24	chr14:24790800-24795200	Strong transcription	Adipose Nuclei	Adipose
25	chr14:24791000-24791400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:24791000-24791400	Weak transcription	K562	blood
27	chr14:24791000-24791800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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