Variant report

Variant	rs9842501
Chromosome Location	chr3:158398281-158398282
allele	C/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	GATA1	chr3:158396838-158398600	K562	blood:	n/a	n/a
2	ARID3A	chr3:158397086-158398388	K562	blood:	n/a	n/a
3	TBL1XR1	chr3:158396980-158398385	K562	blood:	n/a	n/a
4	GATA1	chr3:158396580-158398438	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158395987..158399126-chr3:158405793..158408915,3	K562	blood:
2	chr3:158396822..158398975-chr3:158460109..158461929,2	K562	blood:
3	chr3:158386115..158388967-chr3:158396938..158399014,2	K562	blood:

Variant related genes	Relation type
GFM1	TF binding region
ENSG00000079257	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1047355	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317399	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1367313	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1492908	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1492909	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16829318	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17642107	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17698464	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1812656	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864505	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864506	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2060016	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2060017	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2082157	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2082160	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2082161	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2099198	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115940	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2363659	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3867390	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61376564	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62286646	0.83[EUR][1000 genomes]
rs62288346	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441214	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441215	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441218	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441219	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763018	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6763232	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6763412	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764385	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767485	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767563	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767792	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768290	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779780	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785478	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785658	0.84[AFR][1000 genomes]
rs6791844	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6791847	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800718	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7616819	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7624934	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633910	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7640040	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7648483	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651847	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8650	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs966145	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs966146	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9810874	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813980	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9814061	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815725	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9819575	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9832803	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833067	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835839	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836299	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9839476	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9841	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853503	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853989	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858849	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9859175	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9863232	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9867957	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9869404	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872962	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873022	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873186	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873667	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875043	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875895	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9878187	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9884039	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];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	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9842501	GFM1	cis	Thyroid	GTEx
rs9842501	GFM1	cis	Skin Sun Exposed Lower leg	GTEx
rs9842501	GFM1	cis	Adipose Subcutaneous	GTEx
rs9842501	GFM1	cis	multi-tissue	Pritchard
rs9842501	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs9842501	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs9842501	GFM1	cis	Muscle Skeletal	GTEx
rs9842501	GFM1	cis	Artery Tibial	GTEx
rs9842501	GFM1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158386200-158407800	Weak transcription	HepG2	liver
2	chr3:158390200-158402800	Weak transcription	HSMM	muscle
3	chr3:158390400-158401000	Weak transcription	NHDF-Ad	bronchial
4	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
5	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:158390600-158410600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:158390800-158400000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:158390800-158407800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:158390800-158407800	Weak transcription	Small Intestine	intestine
11	chr3:158390800-158408000	Weak transcription	Brain Anterior Caudate	brain
12	chr3:158390800-158408000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:158390800-158408000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:158390800-158408200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:158390800-158408200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:158390800-158410800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
19	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
20	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
21	chr3:158390800-158427400	Weak transcription	Lung	lung
22	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
26	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
27	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
28	chr3:158390800-158444200	Weak transcription	Gastric	stomach
29	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:158391000-158398400	Weak transcription	Dnd41	blood
31	chr3:158391000-158399000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:158391000-158399800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:158391000-158400000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:158391000-158400000	Weak transcription	Hela-S3	cervix
35	chr3:158391000-158400800	Weak transcription	Osteobl	bone
36	chr3:158391000-158401400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:158391000-158401400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:158391000-158402200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:158391000-158402200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:158391000-158402400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:158391000-158403400	Weak transcription	HMEC	breast
42	chr3:158391000-158407800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:158391000-158408000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:158391000-158409000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:158391000-158409600	Weak transcription	Fetal Kidney	kidney
46	chr3:158391000-158413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
48	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
49	chr3:158391000-158427200	Weak transcription	NHEK	skin
50	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea

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