Variant report

Variant	rs2144494
Chromosome Location	chr14:24773387-24773388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24773334-24773446	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:24773216-24777955	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:24773029-24773524	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24681085..24682828-chr14:24772928..24775361,2	MCF-7	breast:
2	chr14:24773182..24775572-chr14:24899600..24904217,4	MCF-7	breast:
3	chr14:24772236..24774305-chr14:24778506..24780366,3	K562	blood:
4	chr14:24655120..24666858-chr14:24765577..24776253,24	MCF-7	breast:
5	chr14:24765570..24768951-chr14:24773362..24777339,4	K562	blood:
6	chr14:24767097..24775014-chr14:24779936..24787049,14	MCF-7	breast:
7	chr14:24772771..24774909-chr14:24909093..24912015,2	MCF-7	breast:
8	chr14:24769074..24771139-chr14:24772218..24774623,3	K562	blood:

No data

Variant related genes	Relation type
LTB4R2	TF binding region
ENSG00000272658	TF binding region
DHRS1	TF binding region
ENSG00000196943	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000100926	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000100441	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];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158634	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158635	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131941	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886362	0.85[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180196	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs2224122	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224123	0.84[EUR][1000 genomes]
rs2281472	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2516564	0.85[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748543	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181384	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280164	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366641	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374085	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981503	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981504	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]

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	nsv901499	chr14:24765622-24787588	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
4	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
5	nsv564058	chr14:24771285-24786976	Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
6	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2144494	NDRG2	cis	parietal	SCAN
rs2144494	DHRS1	cis	cerebellum	SCAN
rs2144494	LRRC16B	cis	parietal	SCAN
rs2144494	DHRS1	cis	parietal	SCAN
rs2144494	ANG	cis	parietal	SCAN
rs2144494	TGM1	cis	cerebellum	SCAN
rs2144494	LTB4R	cis	lung	GTEx
rs2144494	LTB4R	cis	Thyroid	GTEx
rs2144494	NGDN	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24770200-24777000	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr14:24770200-24778600	Strong transcription	Fetal Stomach	stomach
3	chr14:24770200-24779400	Weak transcription	Right Atrium	heart
4	chr14:24770400-24775400	Genic enhancers	Duodenum Mucosa	Duodenum
5	chr14:24770400-24775600	Genic enhancers	Liver	Liver
6	chr14:24770400-24775600	Genic enhancers	Fetal Intestine Small	intestine
7	chr14:24770400-24775800	Strong transcription	A549	lung
8	chr14:24770400-24777000	Strong transcription	Brain Cingulate Gyrus	brain
9	chr14:24770400-24778800	Weak transcription	Fetal Heart	heart
10	chr14:24770400-24782000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:24770600-24775600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:24770600-24776200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr14:24770600-24776400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:24770600-24776400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr14:24770600-24776400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr14:24770600-24776400	Strong transcription	Fetal Thymus	thymus
17	chr14:24770600-24776600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr14:24770600-24776600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:24770600-24776600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr14:24770600-24776800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:24770600-24776800	Strong transcription	Brain Germinal Matrix	brain
22	chr14:24770600-24777000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:24770600-24777000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr14:24770600-24777000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:24770600-24777000	Strong transcription	Ovary	ovary
26	chr14:24770600-24777000	Strong transcription	HMEC	breast
27	chr14:24770600-24777200	Strong transcription	Brain Hippocampus Middle	brain
28	chr14:24770600-24777200	Strong transcription	Fetal Muscle Leg	muscle
29	chr14:24770600-24777400	Strong transcription	Colon Smooth Muscle	Colon
30	chr14:24770600-24778000	Strong transcription	Thymus	Thymus
31	chr14:24770600-24781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:24770600-24781800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr14:24770800-24773400	Strong transcription	K562	blood
34	chr14:24770800-24773600	Strong transcription	NHDF-Ad	bronchial
35	chr14:24770800-24775200	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr14:24770800-24775600	Strong transcription	Gastric	stomach
37	chr14:24770800-24775600	Strong transcription	Stomach Mucosa	stomach
38	chr14:24770800-24775600	Strong transcription	Osteobl	bone
39	chr14:24770800-24775800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr14:24770800-24775800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr14:24770800-24775800	Strong transcription	Fetal Kidney	kidney
42	chr14:24770800-24775800	Strong transcription	HSMMtube	muscle
43	chr14:24770800-24776000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr14:24770800-24776000	Strong transcription	HSMM	muscle
45	chr14:24770800-24776000	Strong transcription	NH-A	brain
46	chr14:24770800-24776200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr14:24770800-24776400	Strong transcription	Primary B cells from cord blood	blood
48	chr14:24770800-24776400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr14:24770800-24776600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr14:24770800-24776600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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