Variant report

Variant	rs56078503
Chromosome Location	chr3:158454268-158454269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:158454127-158454349	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:158449938..158451943-chr3:158452978..158454973,2	K562	blood:
2	chr3:158450862..158452910-chr3:158453728..158455529,2	K562	blood:
3	chr3:158449492..158452059-chr3:158453554..158456847,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFM1-1	chr3:158453510-158455694	ENSG00000240207.2

No data

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000240207	TF binding region
ENSG00000118855	Chromatin interaction
ENSG00000118849	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12489730	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491877	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12495962	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12497488	0.98[ASN][1000 genomes]
rs1430413	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1430414	0.98[ASN][1000 genomes]
rs1560417	0.98[ASN][1000 genomes]
rs1560418	0.98[ASN][1000 genomes]
rs16829365	0.89[ASN][1000 genomes]
rs17642769	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643171	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643252	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643483	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643581	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643860	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17643917	0.91[ASN][1000 genomes]
rs17699478	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699526	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699997	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700475	0.98[ASN][1000 genomes]
rs2279561	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279562	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307064	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566347	0.98[ASN][1000 genomes]
rs34690420	0.98[ASN][1000 genomes]
rs3863076	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55678388	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55717824	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776609	0.91[ASN][1000 genomes]
rs56023805	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56105525	0.98[ASN][1000 genomes]
rs56152025	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235582	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56261306	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56318834	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57262841	0.98[ASN][1000 genomes]
rs59163359	0.98[ASN][1000 genomes]
rs59173444	0.91[ASN][1000 genomes]
rs60203196	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61138408	0.98[ASN][1000 genomes]
rs61794798	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794799	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794818	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794821	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794822	0.98[ASN][1000 genomes]
rs61794833	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794834	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794835	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61794858	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794859	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796760	0.83[ASN][1000 genomes]
rs61796762	0.98[ASN][1000 genomes]
rs61796764	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796766	0.82[ASN][1000 genomes]
rs61796768	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796770	0.97[ASN][1000 genomes]
rs6441221	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761989	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6783610	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792908	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73158361	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7624420	0.90[ASN][1000 genomes]
rs7624702	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS 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	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56078503	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs56078503	GFM1	cis	Thyroid	GTEx
rs56078503	LXN	cis	multi-tissue	Pritchard
rs56078503	GFM1	cis	Artery Tibial	GTEx
rs56078503	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450400-158460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
4	chr3:158450800-158455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:158450800-158460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
9	chr3:158451000-158455800	Weak transcription	Osteobl	bone
10	chr3:158451000-158457000	Weak transcription	Pancreas	Pancrea
11	chr3:158451000-158458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:158451000-158459800	Weak transcription	Fetal Brain Male	brain
13	chr3:158451000-158459800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:158451000-158460000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
19	chr3:158451000-158464400	Weak transcription	NH-A	brain
20	chr3:158451000-158464800	Weak transcription	Gastric	stomach
21	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
23	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
25	chr3:158452200-158455400	Strong transcription	Fetal Lung	lung
26	chr3:158452200-158456400	Weak transcription	Lung	lung
27	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:158452400-158456800	Weak transcription	Right Ventricle	heart
29	chr3:158453200-158458200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:158453200-158458800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:158453200-158459800	Weak transcription	Ovary	ovary
32	chr3:158453200-158462000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:158453400-158454400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:158453400-158454400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:158453400-158455400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:158453400-158455600	Weak transcription	NHLF	lung
38	chr3:158453400-158455800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:158453400-158459400	Weak transcription	Adipose Nuclei	Adipose
40	chr3:158453400-158460800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:158453400-158462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
45	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:158453600-158454800	Strong transcription	Fetal Intestine Small	intestine
48	chr3:158453600-158455600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:158453600-158455600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:158453600-158456000	Weak transcription	Spleen	Spleen

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