Variant report

Variant	rs6785658
Chromosome Location	chr3:158388394-158388395
allele	G/T
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	CEBPB	chr3:158388227-158388472	HepG2	liver:	n/a	chr3:158388393-158388404
2	CEBPB	chr3:158388250-158388444	K562	blood:	n/a	chr3:158388393-158388404
3	POLR2A	chr3:158381091-158391011	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158387511..158389723-chr3:158444279..158445857,2	MCF-7	breast:
2	chr3:158387127..158389095-chr3:158450464..158453049,2	MCF-7	breast:
3	chr3:158388083..158390320-chr3:158417482..158420125,2	MCF-7	breast:

Variant related genes	Relation type
LXN	TF binding region
ENSG00000118849	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1047355	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13317399	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1367313	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1492908	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1492909	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16829318	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17642107	0.85[EUR][1000 genomes]
rs17698464	0.85[EUR][1000 genomes]
rs1812656	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1864505	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1864506	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060016	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060017	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2082157	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2082160	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2082161	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2099198	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2115940	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2363659	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3867390	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61376564	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62286646	0.81[EUR][1000 genomes]
rs62288346	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441214	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441215	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441218	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441219	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763018	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6763232	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6763412	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6764385	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6767485	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6767563	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6767792	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6768290	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6779780	0.85[EUR][1000 genomes]
rs6785478	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791844	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791847	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6800718	0.83[EUR][1000 genomes]
rs7616819	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7624934	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7633910	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7640040	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7648483	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7651847	0.81[EUR][1000 genomes]
rs8650	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs966145	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs966146	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9810874	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9813980	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9814061	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9815725	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9819575	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9832803	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9833067	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9835839	0.85[AFR][1000 genomes]
rs9836299	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9839476	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9841	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9842501	0.84[AFR][1000 genomes]
rs9853503	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9853989	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9858849	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9859175	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9863232	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9867957	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9869404	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9872962	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9873022	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9873186	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9873667	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9875043	0.80[AFR][1000 genomes]
rs9875895	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9878187	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9884039	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6785658	GFM1	cis	Thyroid	GTEx
rs6785658	GFM1	cis	multi-tissue	Pritchard
rs6785658	GFM1	cis	Esophagus Mucosa	GTEx
rs6785658	GFM1	cis	Skin Sun Exposed Lower leg	GTEx
rs6785658	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6785658	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158389600	Weak transcription	Gastric	stomach
2	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158363200-158389400	Weak transcription	Fetal Brain Male	brain
5	chr3:158363600-158389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:158363800-158388600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:158364000-158388400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:158364400-158388600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:158364800-158391000	Strong transcription	Dnd41	blood
10	chr3:158372200-158389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:158374600-158389400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:158375000-158389400	Weak transcription	Stomach Mucosa	stomach
13	chr3:158376000-158388600	Strong transcription	Fetal Thymus	thymus
14	chr3:158376600-158388400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:158376600-158388600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:158376600-158388600	Strong transcription	Adipose Nuclei	Adipose
17	chr3:158376600-158389000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:158376600-158389400	Strong transcription	K562	blood
19	chr3:158376600-158390200	Strong transcription	HSMM	muscle
20	chr3:158377000-158389600	Weak transcription	Pancreas	Pancrea
21	chr3:158378200-158388400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:158378800-158388400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:158379400-158389000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:158379400-158389400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:158379400-158389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:158379400-158389800	Weak transcription	Right Ventricle	heart
27	chr3:158379400-158389800	Weak transcription	Spleen	Spleen
28	chr3:158379600-158389200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:158379600-158389200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:158379600-158389800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:158379800-158389400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:158380000-158388400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:158381600-158389800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:158381800-158389000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:158382400-158389400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:158382600-158389600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:158382600-158389600	Weak transcription	Lung	lung
38	chr3:158382800-158389400	Weak transcription	Thymus	Thymus
39	chr3:158382800-158389600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:158382800-158389800	Weak transcription	Esophagus	oesophagus
41	chr3:158383000-158389600	Weak transcription	Ovary	ovary
42	chr3:158383800-158388800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:158384800-158389400	Weak transcription	NHEK	skin
44	chr3:158384800-158389800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:158385000-158389000	Weak transcription	Hela-S3	cervix
46	chr3:158385600-158389800	Weak transcription	Psoas Muscle	Psoas
47	chr3:158385600-158390000	Weak transcription	Aorta	Aorta
48	chr3:158385800-158388400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:158385800-158389600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:158386000-158389000	Weak transcription	HSMMtube	muscle

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