Variant report

Variant	rs4142940
Chromosome Location	chr1:220379503-220379504
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220378470..220380460-chr1:220408418..220411307,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10863537	0.82[JPT][hapmap]
rs10863538	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11118507	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026681	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1397958	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1588578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2221833	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667967	0.82[EUR][1000 genomes]
rs2667968	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667969	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667970	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789788	0.81[ASW][hapmap]
rs2789789	0.81[ASW][hapmap]
rs2789792	0.93[ASW][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs2808008	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808009	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2808011	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808012	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808013	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808016	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808018	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2808019	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2808026	0.93[ASW][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs2814492	0.90[ASN][1000 genomes]
rs2814494	0.81[ASN][1000 genomes]
rs2814495	0.89[ASN][1000 genomes]
rs4511114	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541127	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696985	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7535619	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4142940	MOSC2	cis	lymphoblastoid	seeQTL
rs4142940	BPNT1	cis	cerebellum	SCAN
rs4142940	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220325000-220398400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:220345400-220391400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:220348000-220386800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:220350000-220386200	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:220350600-220387800	Weak transcription	Stomach Mucosa	stomach
6	chr1:220353200-220386600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:220353800-220386400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:220354400-220386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:220358000-220381600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:220358000-220382000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:220358600-220385800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:220359000-220385000	Strong transcription	Liver	Liver
13	chr1:220359200-220386000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:220359400-220385800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:220359400-220386800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:220366200-220392000	Weak transcription	Brain Angular Gyrus	brain
17	chr1:220366400-220379800	Weak transcription	Esophagus	oesophagus
18	chr1:220368600-220383800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:220370000-220385200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:220370800-220380400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:220371000-220380400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:220371000-220380600	Strong transcription	Placenta	Placenta
23	chr1:220371400-220385400	Strong transcription	Adipose Nuclei	Adipose
24	chr1:220372000-220381400	Strong transcription	Fetal Thymus	thymus
25	chr1:220372600-220381200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:220372600-220386200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:220373200-220384800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:220373200-220392400	Weak transcription	Fetal Brain Female	brain
29	chr1:220374400-220382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:220374400-220383800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:220374400-220392200	Weak transcription	Fetal Heart	heart
32	chr1:220374600-220407600	Weak transcription	Fetal Brain Male	brain
33	chr1:220375400-220380800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:220375400-220381200	Strong transcription	HSMM	muscle
35	chr1:220375600-220393400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:220375800-220383600	Weak transcription	Fetal Stomach	stomach
37	chr1:220376400-220383800	Weak transcription	Fetal Intestine Small	intestine
38	chr1:220376600-220383000	Weak transcription	HMEC	breast
39	chr1:220377000-220381000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:220377200-220385600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:220378000-220386200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:220378200-220380200	Strong transcription	Fetal Kidney	kidney
43	chr1:220378200-220381200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:220378200-220381400	Strong transcription	Primary T cells from cord blood	blood
45	chr1:220378200-220381400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:220378200-220382200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:220378200-220384800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:220378200-220385600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:220378200-220385600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:220378200-220385600	Strong transcription	Dnd41	blood

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