Variant report

Variant	rs61794821
Chromosome Location	chr3:158460936-158460937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:158460839-158461355	SK-N-MC	brain:	n/a	n/a
2	IRF1	chr3:158460698-158462077	K562	blood:	n/a	n/a
3	CTCF	chr3:158460860-158461010	NHDF-neo	bronchial:	n/a	n/a
4	CTCF	chr3:158460800-158460950	AG10803	skin:	n/a	n/a
5	GATA1	chr3:158460458-158462638	PBDE	blood:	n/a	chr3:158461541-158461549
6	POLR2A	chr3:158460886-158460938	Hela-S3	cervix:	n/a	n/a
7	E2F4	chr3:158460730-158461035	MCF10A-Er-Src	breast:	n/a	n/a
8	IRF1	chr3:158460842-158462121	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158458577..158461138-chr3:158482458..158485038,2	MCF-7	breast:
2	chr3:158459939..158462233-chr3:158502381..158504216,2	K562	blood:
3	chr3:158460933..158463789-chr3:158476160..158478339,2	MCF-7	breast:
4	chr3:158459480..158463209-chr3:158487377..158489850,3	K562	blood:
5	chr3:158460432..158463056-chr3:160166274..160168352,2	K562	blood:
6	chr3:158436485..158439258-chr3:158460195..158462698,2	MCF-7	breast:
7	chr3:158460803..158463354-chr3:158491708..158495775,3	MCF-7	breast:
8	chr3:158449518..158452301-chr3:158459445..158461746,2	K562	blood:
9	chr3:158460535..158463569-chr3:158485290..158488167,3	MCF-7	breast:
10	chr3:158459999..158462201-chr3:158488289..158489844,2	MCF-7	breast:
11	chr3:158396822..158398975-chr3:158460109..158461929,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFM1-1	chr3:158460570-158461381	ENSG00000240207.1
2	lnc-GFM1-1	chr3:158460570-158461125	ENSG00000240207.1

No data

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000118849	Chromatin interaction
ENSG00000118855	Chromatin interaction
ENSG00000213186	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12489730	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491877	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12495962	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12497488	0.98[ASN][1000 genomes]
rs1430413	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1430414	0.98[ASN][1000 genomes]
rs1560417	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1560418	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16829365	0.89[ASN][1000 genomes]
rs17642769	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643171	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17643252	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643483	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643581	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643860	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17643917	0.91[ASN][1000 genomes]
rs17699478	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699526	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699997	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700475	0.98[ASN][1000 genomes]
rs2279561	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279562	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307064	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566347	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34690420	0.98[ASN][1000 genomes]
rs3863076	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55678388	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55717824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776609	0.91[ASN][1000 genomes]
rs56023805	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56078503	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105525	0.98[ASN][1000 genomes]
rs56152025	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235582	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56261306	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56318834	0.89[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	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61138408	0.98[ASN][1000 genomes]
rs61794798	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794799	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794818	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794822	0.98[ASN][1000 genomes]
rs61794833	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794834	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794835	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61794858	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794859	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796760	0.83[ASN][1000 genomes]
rs61796762	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796764	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796766	0.82[ASN][1000 genomes]
rs61796768	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61796770	0.97[ASN][1000 genomes]
rs6441221	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761989	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6783610	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792908	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73158361	0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61794821	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs61794821	GFM1	cis	Thyroid	GTEx
rs61794821	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
3	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
6	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
10	chr3:158451000-158464400	Weak transcription	NH-A	brain
11	chr3:158451000-158464800	Weak transcription	Gastric	stomach
12	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
14	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:158453200-158462000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:158453400-158462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
23	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:158453600-158462000	Weak transcription	Brain Anterior Caudate	brain
26	chr3:158453600-158462600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:158453600-158464000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
30	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:158456400-158461600	Weak transcription	Osteobl	bone
32	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:158457000-158464600	Weak transcription	HSMM	muscle
34	chr3:158457200-158464800	Weak transcription	Spleen	Spleen
35	chr3:158457200-158468200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
37	chr3:158457800-158464800	Weak transcription	Hela-S3	cervix
38	chr3:158457800-158466000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
40	chr3:158458000-158464800	Weak transcription	HSMMtube	muscle
41	chr3:158458000-158471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:158458800-158464600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:158459200-158462200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:158459400-158461000	Strong transcription	Adipose Nuclei	Adipose
45	chr3:158459400-158464800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:158459600-158465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:158459600-158465600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:158459600-158468400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:158459800-158461000	Strong transcription	Liver	Liver
50	chr3:158459800-158461000	Genic enhancers	K562	blood

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