Variant report

Variant	rs729421
Chromosome Location	chr14:24736961-24736962
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	chr14:24736897-24737095	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:24736862-24737065	GM12878	blood:	n/a	n/a
3	POLR2A	chr14:24736527-24737054	HepG2	liver:	n/a	n/a
4	POLR2A	chr14:24736678-24737174	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24734952..24736987-chr14:24899499..24901815,2	MCF-7	breast:
2	chr14:24680938..24683854-chr14:24736234..24738459,2	K562	blood:
3	chr14:24658044..24659944-chr14:24736263..24737980,2	MCF-7	breast:
4	chr14:24731299..24737661-chr14:24737668..24742603,15	K562	blood:

Variant related genes	Relation type
TGM1	TF binding region
RABGGTA	TF binding region
ENSG00000254505	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000196497	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11158621	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14193	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075530	0.83[JPT][hapmap]
rs2281473	0.83[JPT][hapmap]
rs2295313	0.85[EUR][1000 genomes]
rs3825585	0.83[JPT][hapmap]
rs3940231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982886	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982887	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573653	0.83[JPT][hapmap]
rs941502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941503	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941505	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs729421	ADCY4	cis	cerebellum	SCAN
rs729421	ANG	cis	parietal	SCAN
rs729421	RABGGTA	Cis_1M	lymphoblastoid	RTeQTL
rs729421	DHRS1	cis	parietal	SCAN
rs729421	RABGGTA	cis	multi-tissue	Pritchard
rs729421	TSSK4	cis	parietal	SCAN
rs729421	FAM158A	cis	parietal	SCAN
rs729421	DHRS1	cis	cerebellum	SCAN
rs729421	PSMB11	cis	parietal	SCAN
rs729421	MYH6	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24712600-24740000	Weak transcription	Small Intestine	intestine
2	chr14:24713000-24740000	Weak transcription	Right Atrium	heart
3	chr14:24716400-24739800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:24716600-24739800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:24720000-24739600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:24721200-24739400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr14:24721600-24739800	Weak transcription	HUVEC	blood vessel
8	chr14:24722600-24740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:24725800-24737800	Weak transcription	Psoas Muscle	Psoas
10	chr14:24726200-24739800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:24726800-24739800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:24727800-24739800	Weak transcription	K562	blood
13	chr14:24728400-24739800	Strong transcription	Fetal Intestine Small	intestine
14	chr14:24729000-24738000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:24729000-24739800	Weak transcription	NH-A	brain
16	chr14:24729000-24740000	Weak transcription	HSMM	muscle
17	chr14:24729200-24738800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:24729600-24739600	Strong transcription	Fetal Stomach	stomach
19	chr14:24729600-24739800	Weak transcription	A549	lung
20	chr14:24729800-24739800	Weak transcription	Hela-S3	cervix
21	chr14:24731800-24739200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:24732000-24739400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr14:24732000-24739600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr14:24732000-24739600	Strong transcription	Lung	lung
25	chr14:24732600-24740000	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:24732800-24739000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:24732800-24739000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr14:24732800-24739600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:24732800-24739800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr14:24733200-24737200	Strong transcription	Brain Substantia Nigra	brain
31	chr14:24733200-24739200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr14:24733200-24739400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr14:24733200-24739400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:24733200-24740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:24733400-24739200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr14:24733800-24737200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr14:24733800-24739000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr14:24733800-24739200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr14:24733800-24739400	Strong transcription	HepG2	liver
40	chr14:24733800-24739800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr14:24734000-24737000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr14:24734000-24738800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr14:24734000-24738800	Strong transcription	Brain Hippocampus Middle	brain
44	chr14:24734000-24739200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:24734000-24739400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr14:24734000-24739400	Strong transcription	Fetal Muscle Leg	muscle
47	chr14:24734200-24737600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:24734200-24738000	Strong transcription	Brain Germinal Matrix	brain
49	chr14:24734200-24738200	Strong transcription	Fetal Brain Female	brain
50	chr14:24734200-24738800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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