Variant report

Variant	rs17699478
Chromosome Location	chr3:158426243-158426244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158425598..158427216-chr3:158443542..158445810,2	K562	blood:
2	chr3:158389157..158390779-chr3:158425576..158427091,2	MCF-7	breast:
3	chr3:158415231..158418143-chr3:158424169..158428339,3	MCF-7	breast:
4	chr3:158423211..158426282-chr3:158428433..158432187,3	K562	blood:

Variant related genes	Relation type
ENSG00000079257	Chromatin interaction
ENSG00000118849	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10513528	0.86[YRI][hapmap]
rs12489730	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491877	0.94[ASN][1000 genomes]
rs12495962	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12497488	0.95[ASN][1000 genomes]
rs1430413	0.95[ASN][1000 genomes]
rs1430414	0.95[ASN][1000 genomes]
rs1560417	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs1560418	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs16829365	0.89[ASN][1000 genomes]
rs17630607	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17630980	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17642769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643252	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643483	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643581	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643860	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17643917	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17697458	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs17698494	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17699103	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17699324	0.81[ASW][hapmap];0.90[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17699526	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699997	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17700122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700475	0.95[ASN][1000 genomes]
rs1864506	0.82[CHD][hapmap]
rs2060017	0.82[CHD][hapmap]
rs2279561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304408	0.90[CEU][hapmap]
rs2307064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566347	0.95[ASN][1000 genomes]
rs28372852	0.82[AMR][1000 genomes]
rs34690420	0.95[ASN][1000 genomes]
rs3863076	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3867391	0.81[ASW][hapmap];0.90[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41434057	0.86[YRI][hapmap]
rs55666734	0.82[AMR][1000 genomes]
rs55678388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55705231	0.94[ASN][1000 genomes]
rs55717824	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55776609	0.88[ASN][1000 genomes]
rs56023805	0.95[ASN][1000 genomes]
rs56075263	0.80[AMR][1000 genomes]
rs56078503	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089835	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56105525	0.95[ASN][1000 genomes]
rs56152025	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56167308	0.82[AMR][1000 genomes]
rs56235582	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56261306	0.95[ASN][1000 genomes]
rs56318834	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57262841	0.95[ASN][1000 genomes]
rs59163359	0.95[ASN][1000 genomes]
rs59173444	0.89[ASN][1000 genomes]
rs60203196	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60942689	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61138408	0.95[ASN][1000 genomes]
rs61794798	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794799	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794818	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61794821	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61794822	0.95[ASN][1000 genomes]
rs61794833	0.95[ASN][1000 genomes]
rs61794834	0.95[ASN][1000 genomes]
rs61794835	0.91[ASN][1000 genomes]
rs61794858	0.95[ASN][1000 genomes]
rs61794859	0.95[ASN][1000 genomes]
rs61796762	0.95[ASN][1000 genomes]
rs61796764	0.94[ASN][1000 genomes]
rs61796768	0.94[ASN][1000 genomes]
rs61796770	0.94[ASN][1000 genomes]
rs62286650	0.82[AMR][1000 genomes]
rs62286654	0.82[AMR][1000 genomes]
rs62288303	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62288305	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288306	0.82[AMR][1000 genomes]
rs62288307	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288344	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62288345	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441208	0.87[CHD][hapmap];0.92[GIH][hapmap]
rs6441215	0.82[CHD][hapmap]
rs6441221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761989	0.95[ASN][1000 genomes]
rs6763412	0.82[CHD][hapmap]
rs6776901	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs6777231	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs6783610	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791847	0.82[CHD][hapmap]
rs6792908	0.95[ASN][1000 genomes]
rs6804230	0.87[CHD][hapmap];0.96[GIH][hapmap]
rs73158361	0.94[ASN][1000 genomes]
rs7610009	0.90[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7624420	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7624702	0.87[ASN][1000 genomes]
rs7624934	0.82[CHD][hapmap]
rs7628497	0.82[AMR][1000 genomes]
rs7633713	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7651847	0.82[CHD][hapmap]
rs9832803	0.82[CHD][hapmap]
rs9842500	0.82[CHD][hapmap]
rs9867957	0.82[CHD][hapmap]
rs9884039	0.82[CHD][hapmap]

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	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
4	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
5	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
6	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
7	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
8	nsv1007141	chr3:158415840-158433128	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17699478	LXN	cis	cerebellum	SCAN
rs17699478	GFM1	cis	Muscle Skeletal	GTEx
rs17699478	GFM1	cis	Nerve Tibial	GTEx
rs17699478	GFM1	cis	cerebellum	SCAN
rs17699478	LXN	cis	parietal	SCAN
rs17699478	LXN	cis	multi-tissue	Pritchard
rs17699478	GFM1	cis	parietal	SCAN
rs17699478	GFM1	cis	Artery Tibial	GTEx
rs17699478	LXN	cis	lymphoblastoid	seeQTL
rs17699478	GFM1	cis	Thyroid	GTEx
rs17699478	GFM1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
5	chr3:158390800-158427400	Weak transcription	Lung	lung
6	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
10	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
11	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
12	chr3:158390800-158444200	Weak transcription	Gastric	stomach
13	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:158391000-158427200	Weak transcription	NHEK	skin
15	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
16	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:158397000-158429200	Weak transcription	Ovary	ovary
20	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
22	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:158400600-158429000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:158408400-158430200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:158408400-158443000	Weak transcription	HepG2	liver
27	chr3:158409000-158429800	Weak transcription	Small Intestine	intestine
28	chr3:158409200-158427400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:158409400-158426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:158409400-158427200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:158410800-158430400	Weak transcription	Fetal Thymus	thymus
33	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:158412000-158427400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:158412200-158427200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:158412400-158427000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
39	chr3:158412600-158426400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
41	chr3:158415800-158429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:158416000-158430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:158416800-158426800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:158416800-158428600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:158417000-158427400	Weak transcription	Left Ventricle	heart
46	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
47	chr3:158420200-158426600	Strong transcription	Fetal Lung	lung
48	chr3:158420600-158429400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:158421000-158427800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:158421200-158427200	Weak transcription	HMEC	breast

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