Variant report

Variant	rs17643581
Chromosome Location	chr3:158446279-158446280
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	CTCF	chr3:158445113-158446319	A549	lung:	n/a	chr3:158445728-158445746 chr3:158445730-158445751 chr3:158445733-158445743 chr3:158445731-158445740 chr3:158445729-158445745
2	CTCF	chr3:158446140-158446290	GM12872	blood:	n/a	n/a
3	CTCF	chr3:158445211-158446295	SK-N-SH	brain:	n/a	chr3:158445728-158445746 chr3:158445730-158445751 chr3:158445733-158445743 chr3:158445731-158445740 chr3:158445729-158445745
4	CTCF	chr3:158446160-158446310	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158444754..158447490-chr3:158487948..158489937,2	MCF-7	breast:
2	chr3:158445761..158447477-chr3:158506240..158508381,2	MCF-7	breast:
3	chr3:158445207..158446704-chr3:158508810..158509868,10	K562	blood:

Variant related genes	Relation type
ENSG00000240207	TF binding region
MFSD1	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12489730	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491877	0.95[ASN][1000 genomes]
rs12495962	0.97[ASN][1000 genomes]
rs12497488	0.97[ASN][1000 genomes]
rs1430413	0.97[ASN][1000 genomes]
rs1430414	0.97[ASN][1000 genomes]
rs1560417	0.97[ASN][1000 genomes]
rs1560418	0.97[ASN][1000 genomes]
rs16829365	0.90[ASN][1000 genomes]
rs17642769	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643171	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643252	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643483	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643860	0.97[ASN][1000 genomes]
rs17643917	0.90[ASN][1000 genomes]
rs17698494	0.80[EUR][1000 genomes]
rs17699103	0.81[EUR][1000 genomes]
rs17699324	0.84[EUR][1000 genomes]
rs17699478	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17699526	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17699997	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700122	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17700475	0.97[ASN][1000 genomes]
rs2279561	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279562	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307064	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2566347	0.97[ASN][1000 genomes]
rs34690420	0.97[ASN][1000 genomes]
rs3863076	0.97[ASN][1000 genomes]
rs3867391	0.83[EUR][1000 genomes]
rs55678388	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55705231	0.95[ASN][1000 genomes]
rs55717824	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55776609	0.90[ASN][1000 genomes]
rs56023805	0.97[ASN][1000 genomes]
rs56078503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56105525	0.97[ASN][1000 genomes]
rs56152025	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235582	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56261306	0.97[ASN][1000 genomes]
rs56318834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57262841	0.97[ASN][1000 genomes]
rs59163359	0.97[ASN][1000 genomes]
rs59173444	0.90[ASN][1000 genomes]
rs60203196	0.97[ASN][1000 genomes]
rs61138408	0.97[ASN][1000 genomes]
rs61794798	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794799	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794818	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794821	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794822	0.97[ASN][1000 genomes]
rs61794833	0.97[ASN][1000 genomes]
rs61794834	0.97[ASN][1000 genomes]
rs61794835	0.92[ASN][1000 genomes]
rs61794858	0.97[ASN][1000 genomes]
rs61794859	0.97[ASN][1000 genomes]
rs61796760	0.82[ASN][1000 genomes]
rs61796762	0.97[ASN][1000 genomes]
rs61796764	0.95[ASN][1000 genomes]
rs61796766	0.80[ASN][1000 genomes]
rs61796768	0.95[ASN][1000 genomes]
rs61796770	0.95[ASN][1000 genomes]
rs6441221	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761989	0.97[ASN][1000 genomes]
rs6783610	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792908	0.97[ASN][1000 genomes]
rs73158361	0.95[ASN][1000 genomes]
rs7610009	0.83[EUR][1000 genomes]
rs7624420	0.88[ASN][1000 genomes]
rs7624702	0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17643581	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs17643581	GFM1	cis	Artery Tibial	GTEx
rs17643581	GFM1	cis	Nerve Tibial	GTEx
rs17643581	GFM1	cis	Thyroid	GTEx
rs17643581	LXN	cis	multi-tissue	Pritchard
rs17643581	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs17643581	GFM1	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
2	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:158431000-158449200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:158432200-158449200	Weak transcription	Pancreas	Pancrea
5	chr3:158435000-158449200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:158439200-158449200	Weak transcription	Fetal Brain Female	brain
7	chr3:158440600-158446400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:158440800-158446800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr3:158441000-158449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:158441000-158449200	Weak transcription	Esophagus	oesophagus
11	chr3:158441400-158449000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:158442200-158449000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:158443200-158449400	Weak transcription	Psoas Muscle	Psoas
14	chr3:158443200-158449400	Weak transcription	Spleen	Spleen
15	chr3:158443800-158447200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:158443800-158449200	Weak transcription	Left Ventricle	heart
17	chr3:158443800-158449600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:158444000-158449400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:158444200-158449200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:158444400-158449400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:158445200-158447000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:158445400-158446400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:158445400-158446400	Enhancers	Fetal Muscle Leg	muscle
24	chr3:158445400-158446800	Enhancers	Fetal Intestine Large	intestine
25	chr3:158445400-158446800	Enhancers	Fetal Kidney	kidney
26	chr3:158445400-158449600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:158445600-158447600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:158445600-158448600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:158445600-158449200	Weak transcription	Lung	lung
30	chr3:158445600-158449200	Weak transcription	HSMMtube	muscle
31	chr3:158445600-158449400	Weak transcription	Gastric	stomach
32	chr3:158445600-158449400	Weak transcription	Right Atrium	heart
33	chr3:158445800-158449400	Weak transcription	HSMM	muscle
34	chr3:158446000-158447000	Enhancers	NHLF	lung
35	chr3:158446000-158449000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:158446000-158449000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:158446000-158449000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:158446000-158449000	Weak transcription	GM12878-XiMat	blood
39	chr3:158446000-158449000	Weak transcription	NH-A	brain
40	chr3:158446000-158449000	Weak transcription	NHEK	skin
41	chr3:158446000-158449200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:158446000-158449400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:158446200-158446400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:158446200-158446800	Enhancers	Fetal Lung	lung
45	chr3:158446200-158446800	Enhancers	A549	lung
46	chr3:158446200-158447000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:158446200-158447000	Enhancers	Rectal Smooth Muscle	rectum
48	chr3:158446200-158447000	Enhancers	Osteobl	bone
49	chr3:158446200-158447600	Weak transcription	Fetal Intestine Small	intestine
50	chr3:158446200-158448800	Weak transcription	Fetal Stomach	stomach

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