Variant report

Variant	rs1542140
Chromosome Location	chr1:211840278-211840279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211840072..211841886-chr1:211843457..211846340,2	MCF-7	breast:
2	chr1:211837374..211840325-chr1:211844440..211846653,2	K562	blood:
3	chr1:211830163..211831945-chr1:211837161..211840904,3	K562	blood:
4	chr1:211750670..211753055-chr1:211839773..211842017,2	K562	blood:

Variant related genes	Relation type
ENSG00000170385	Chromatin interaction
ENSG00000117650	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1067248	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1067249	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1067250	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1822568	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587487	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2794730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs701918	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs701921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs701922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs785316	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785317	0.87[ASN][1000 genomes]
rs785318	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894852	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1542140	MAPKAPK2	cis	parietal	SCAN
rs1542140	LAMB3	cis	cerebellum	SCAN
rs1542140	IRF6	cis	cerebellum	SCAN
rs1542140	C1orf186	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211827600-211847600	Weak transcription	HSMM	muscle
2	chr1:211827600-211847600	Weak transcription	NHEK	skin
3	chr1:211828200-211840400	Weak transcription	Fetal Lung	lung
4	chr1:211828600-211842400	Weak transcription	NHLF	lung
5	chr1:211828600-211842800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:211828600-211845600	Weak transcription	Fetal Heart	heart
7	chr1:211828600-211847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:211828600-211847600	Weak transcription	Brain Germinal Matrix	brain
9	chr1:211828600-211847800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:211828600-211847800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:211828600-211848000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:211828600-211848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:211828800-211841800	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:211828800-211847600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:211829000-211842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:211829000-211847400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:211829000-211847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:211829200-211840800	Weak transcription	Fetal Intestine Large	intestine
19	chr1:211829600-211848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:211831400-211842400	Weak transcription	Fetal Stomach	stomach
21	chr1:211832400-211847600	Weak transcription	Primary B cells from cord blood	blood
22	chr1:211833200-211847800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:211833600-211845800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:211833800-211847000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:211835200-211846400	Strong transcription	Fetal Thymus	thymus
26	chr1:211835400-211844800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:211835400-211845200	Strong transcription	Dnd41	blood
28	chr1:211835400-211847400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:211835800-211844600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:211835800-211844800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:211836000-211844600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:211836400-211845000	Strong transcription	A549	lung
33	chr1:211836600-211844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:211836600-211846800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:211837000-211842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:211837200-211842200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:211837200-211848000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:211837400-211844400	Strong transcription	Hela-S3	cervix
39	chr1:211837400-211848000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:211837600-211845200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:211837600-211846800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:211837600-211847000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:211837600-211847600	Weak transcription	Fetal Kidney	kidney
44	chr1:211837800-211841000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:211837800-211841000	Strong transcription	NHDF-Ad	bronchial
46	chr1:211837800-211844400	Strong transcription	GM12878-XiMat	blood
47	chr1:211837800-211844800	Strong transcription	Osteobl	bone
48	chr1:211838000-211840800	Weak transcription	Stomach Mucosa	stomach
49	chr1:211838000-211844800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:211838400-211848000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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