Variant report

Variant	rs17699456
Chromosome Location	chr3:158426185-158426186
allele	C/G
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
ENSG00000118849	Chromatin interaction
ENSG00000079257	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006911	0.86[YRI][hapmap]
rs1047366	0.83[CEU][hapmap];0.80[YRI][hapmap]
rs12639052	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs1864507	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs2253249	0.82[YRI][hapmap]
rs2303909	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs2364927	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2566346	0.96[ASN][1000 genomes]
rs3851362	0.83[CEU][hapmap]
rs4680460	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4875	0.83[CEU][hapmap]
rs57932243	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61794797	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441224	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6772483	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs6783879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800914	0.84[CEU][hapmap]
rs6803047	0.84[CEU][hapmap]
rs6804249	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804259	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs7618110	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621897	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs7635993	0.83[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8455	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs891464	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs9819567	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs9822005	0.85[YRI][hapmap]
rs9825696	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9840571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861938	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs9863103	0.83[CHB][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs9866134	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17699456	MLF1	cis	Heart Left Ventricle	GTEx
rs17699456	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:158409400-158426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:158409400-158426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:158409400-158427200	Weak transcription	Brain Anterior Caudate	brain
32	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:158410800-158430400	Weak transcription	Fetal Thymus	thymus
34	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:158412000-158426200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:158412000-158427400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:158412200-158426200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:158412200-158427200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:158412400-158427000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
42	chr3:158412600-158426400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
44	chr3:158415800-158429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:158416000-158430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:158416800-158426800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:158416800-158428600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:158417000-158427400	Weak transcription	Left Ventricle	heart
49	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
50	chr3:158420200-158426600	Strong transcription	Fetal Lung	lung

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