Variant report

Variant	rs2422139
Chromosome Location	chr1:172390896-172390897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489286	1.00[ASN][1000 genomes]
rs1052256	1.00[ASN][1000 genomes]
rs10752953	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132148	1.00[ASN][1000 genomes]
rs12031216	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277932	1.00[ASN][1000 genomes]
rs17369011	1.00[ASN][1000 genomes]
rs2001131	0.92[CEU][hapmap]
rs2051628	0.94[CEU][hapmap]
rs2157451	1.00[CEU][hapmap]
rs2213739	1.00[CEU][hapmap]
rs2230471	1.00[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2422142	0.82[CEU][hapmap]
rs4916185	1.00[ASN][1000 genomes]
rs4916255	1.00[ASN][1000 genomes]
rs4916256	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916259	0.94[CEU][hapmap]
rs56259646	1.00[ASN][1000 genomes]
rs56340136	1.00[ASN][1000 genomes]
rs61806074	1.00[ASN][1000 genomes]
rs61806089	1.00[ASN][1000 genomes]
rs61806090	1.00[ASN][1000 genomes]
rs61806091	1.00[ASN][1000 genomes]
rs6660051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667786	0.82[CEU][hapmap]
rs6674018	1.00[ASN][1000 genomes]
rs6683444	0.93[CEU][hapmap]
rs6700880	0.94[CEU][hapmap]
rs916365	0.94[CEU][hapmap]
rs9425307	1.00[ASN][1000 genomes]
rs9425309	1.00[ASN][1000 genomes]
rs9425314	1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425315	1.00[ASN][1000 genomes]
rs9425610	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425618	1.00[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs978875	1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2422139	TNFSF4	cis	brain	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172384400-172398400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:172385000-172391600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:172385800-172391000	Weak transcription	Fetal Lung	lung
5	chr1:172385800-172411000	Weak transcription	Fetal Stomach	stomach
6	chr1:172386000-172391200	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:172386800-172391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:172387200-172392200	Enhancers	Primary T cells from cord blood	blood
9	chr1:172387400-172391000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:172387600-172392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:172387600-172392400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:172388600-172392200	Weak transcription	NHEK	skin
13	chr1:172388800-172392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:172388800-172392200	Weak transcription	HMEC	breast
15	chr1:172389800-172391400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:172390000-172391000	Weak transcription	Fetal Thymus	thymus
17	chr1:172390000-172391400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:172390200-172391200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:172390200-172391800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:172390400-172391000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:172390400-172391200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:172390400-172395600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:172390600-172391200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:172390600-172391200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:172390600-172391400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:172390600-172391600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:172390600-172395600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:172390800-172391000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:172390800-172391200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr1:172390800-172391400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:172390800-172391400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:172390800-172391400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:172390800-172391600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:172390800-172391800	Enhancers	Brain Anterior Caudate	brain
35	chr1:172390800-172392000	Enhancers	Brain Cingulate Gyrus	brain
36	chr1:172390800-172392000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:172390800-172392000	Enhancers	Brain Substantia Nigra	brain
38	chr1:172390800-172392200	Enhancers	Brain Hippocampus Middle	brain
39	chr1:172390800-172392200	Enhancers	Psoas Muscle	Psoas

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