Variant report

Variant	rs12639052
Chromosome Location	chr3:158368524-158368525
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158362024..158365390-chr3:158367743..158370169,5	MCF-7	breast:
2	chr3:158288125..158290647-chr3:158366805..158369769,2	MCF-7	breast:
3	chr3:158367114..158369104-chr3:158370938..158373936,5	K562	blood:
4	chr3:158361174..158366807-chr3:158367896..158374332,10	K562	blood:
5	chr3:158366809..158369003-chr3:158371000..158374094,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243150	Chromatin interaction
ENSG00000168827	Chromatin interaction
ENSG00000178053	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1038886	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1047366	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1075551	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10936158	0.94[EUR][1000 genomes]
rs12107643	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12496174	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13324770	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13325932	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1369563	0.81[EUR][1000 genomes]
rs1435642	0.85[YRI][hapmap]
rs1602760	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1656376	0.85[YRI][hapmap]
rs17629360	0.81[EUR][1000 genomes]
rs17629390	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs17629414	0.80[EUR][1000 genomes]
rs17699456	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs1836688	0.87[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1864503	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1864507	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2115943	0.81[EUR][1000 genomes]
rs2303909	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2364274	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2731112	0.85[YRI][hapmap]
rs28481597	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3765025	0.88[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs3845272	0.89[EUR][1000 genomes]
rs3851361	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3851362	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs3851363	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4680445	0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs4680449	0.98[EUR][1000 genomes]
rs4680450	0.87[EUR][1000 genomes]
rs4680451	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4680452	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4680453	0.97[EUR][1000 genomes]
rs4680457	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4680460	0.82[CEU][hapmap]
rs4875	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6441212	0.98[EUR][1000 genomes]
rs6441220	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6771248	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6772483	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6781342	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6783879	0.83[CEU][hapmap]
rs6800914	0.96[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6802317	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6803047	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6803608	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6804249	0.82[CEU][hapmap];0.81[YRI][hapmap]
rs6804259	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7613814	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs7621897	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7631310	0.87[CEU][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs7635993	0.81[YRI][hapmap]
rs7653826	0.98[EUR][1000 genomes]
rs8455	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs891464	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9819567	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9819631	0.80[EUR][1000 genomes]
rs9824985	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9840571	0.82[CEU][hapmap]
rs9848908	0.81[EUR][1000 genomes]
rs9864508	0.80[EUR][1000 genomes]
rs9866134	0.82[CEU][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12639052	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs12639052	MLF1	cis	Heart Left Ventricle	GTEx
rs12639052	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158369800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:158362800-158389600	Weak transcription	Gastric	stomach
3	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:158363000-158369800	Weak transcription	Aorta	Aorta
6	chr3:158363000-158369800	Weak transcription	Lung	lung
7	chr3:158363000-158370400	Weak transcription	Pancreas	Pancrea
8	chr3:158363000-158376600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:158363000-158378200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:158363000-158379800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:158363000-158381800	Weak transcription	Esophagus	oesophagus
12	chr3:158363200-158370200	Weak transcription	Colonic Mucosa	Colon
13	chr3:158363200-158378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:158363200-158389400	Weak transcription	Fetal Brain Male	brain
15	chr3:158363400-158369800	Weak transcription	Small Intestine	intestine
16	chr3:158363400-158370400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:158363400-158374200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:158363400-158376600	Weak transcription	Fetal Kidney	kidney
19	chr3:158363600-158369200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:158363600-158369800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:158363600-158369800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:158363600-158376600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:158363600-158379000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:158363600-158389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:158363800-158369400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:158363800-158374800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:158363800-158375000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:158363800-158375800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:158363800-158388200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:158363800-158388600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:158364000-158368600	Strong transcription	NHDF-Ad	bronchial
32	chr3:158364000-158374800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:158364000-158375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:158364000-158375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:158364000-158375200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:158364000-158375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:158364000-158377600	Strong transcription	Osteobl	bone
38	chr3:158364000-158385400	Weak transcription	Fetal Heart	heart
39	chr3:158364000-158387400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:158364000-158388400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr3:158364200-158370000	Weak transcription	Brain Substantia Nigra	brain
42	chr3:158364200-158370000	Weak transcription	GM12878-XiMat	blood
43	chr3:158364200-158374600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:158364200-158375200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:158364200-158377200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:158364200-158378600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:158364200-158379000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:158364200-158385800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:158364200-158388200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:158364400-158374200	Strong transcription	A549	lung

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