Variant report

Variant	rs17699997
Chromosome Location	chr3:158439496-158439497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158438560..158442755-chr3:158443852..158445905,3	K562	blood:
2	chr3:158415825..158417591-chr3:158438376..158440279,2	MCF-7	breast:
3	chr3:158439350..158441066-chr3:158462153..158464983,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12489730	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491877	0.95[ASN][1000 genomes]
rs12495962	0.80[AFR][1000 genomes];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]
rs17630980	0.80[EUR][1000 genomes]
rs17642769	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643171	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643483	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643581	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643860	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17643917	0.90[ASN][1000 genomes]
rs17698494	0.81[EUR][1000 genomes]
rs17699103	0.83[EUR][1000 genomes]
rs17699324	0.86[EUR][1000 genomes]
rs17699478	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17699526	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17700475	0.97[ASN][1000 genomes]
rs2279561	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279562	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307064	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2566347	0.97[ASN][1000 genomes]
rs34690420	0.97[ASN][1000 genomes]
rs3863076	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3867391	0.84[EUR][1000 genomes]
rs55678388	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55705231	0.95[ASN][1000 genomes]
rs55717824	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55776609	0.90[ASN][1000 genomes]
rs56023805	0.97[ASN][1000 genomes]
rs56078503	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56089835	0.80[EUR][1000 genomes]
rs56105525	0.97[ASN][1000 genomes]
rs56152025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235582	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56261306	0.97[ASN][1000 genomes]
rs56318834	0.91[AMR][1000 genomes];0.97[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	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs60942689	0.80[EUR][1000 genomes]
rs61138408	0.97[ASN][1000 genomes]
rs61794798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794818	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794821	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[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]
rs62288305	0.80[EUR][1000 genomes]
rs62288307	0.80[EUR][1000 genomes]
rs62288344	0.80[EUR][1000 genomes]
rs62288345	0.80[EUR][1000 genomes]
rs6441221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761989	0.97[ASN][1000 genomes]
rs6783610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792908	0.97[ASN][1000 genomes]
rs73158361	0.95[ASN][1000 genomes]
rs7610009	0.84[EUR][1000 genomes]
rs7624420	0.88[ASN][1000 genomes]
rs7624702	0.88[ASN][1000 genomes]
rs7633713	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17699997	GFM1	cis	Nerve Tibial	GTEx
rs17699997	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs17699997	GFM1	cis	Thyroid	GTEx
rs17699997	GFM1	cis	Artery Tibial	GTEx
rs17699997	GFM1	cis	Muscle Skeletal	GTEx
rs17699997	GFM1	cis	Esophagus Mucosa	GTEx
rs17699997	LXN	cis	multi-tissue	Pritchard
rs17699997	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158444200	Weak transcription	Gastric	stomach
2	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
5	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:158408400-158443000	Weak transcription	HepG2	liver
7	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
9	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
10	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:158427600-158440600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:158427800-158440400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:158427800-158440600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:158427800-158440800	Weak transcription	Liver	Liver
15	chr3:158427800-158440800	Weak transcription	Esophagus	oesophagus
16	chr3:158429000-158440600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:158429800-158440800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:158430600-158440800	Weak transcription	Small Intestine	intestine
20	chr3:158431000-158439600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:158431000-158439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:158431000-158440600	Weak transcription	Fetal Thymus	thymus
23	chr3:158431000-158442000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:158431000-158442400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:158431000-158444200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:158431000-158445400	Weak transcription	GM12878-XiMat	blood
27	chr3:158431000-158449200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:158431200-158445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:158431200-158445800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:158431400-158445400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:158431400-158445400	Weak transcription	Dnd41	blood
32	chr3:158432000-158445400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:158432000-158445400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:158432200-158440600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:158432200-158444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:158432200-158445400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:158432200-158445800	Weak transcription	Brain Substantia Nigra	brain
38	chr3:158432200-158449200	Weak transcription	Pancreas	Pancrea
39	chr3:158432400-158440600	Weak transcription	Lung	lung
40	chr3:158432400-158442600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:158433200-158440600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:158433400-158440400	Weak transcription	Primary B cells from cord blood	blood
43	chr3:158433800-158440800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:158433800-158442800	Weak transcription	Spleen	Spleen
45	chr3:158434000-158440600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:158434000-158442600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:158435000-158443400	Weak transcription	NHEK	skin
48	chr3:158435000-158449200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:158435200-158439800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:158435200-158440800	Weak transcription	Colon Smooth Muscle	Colon

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