Variant report

Variant	rs6137927
Chromosome Location	chr20:23372513-23372514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625160	0.85[JPT][hapmap]
rs12625164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.85[JPT][hapmap]
rs17757228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17757442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17830281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2277765	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2281428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3736755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3761274	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55851398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56094936	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56334525	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6036423	0.81[JPT][hapmap]
rs6036424	0.84[JPT][hapmap]
rs6048803	0.89[JPT][hapmap]
rs6106669	0.84[JPT][hapmap]
rs6114094	0.89[JPT][hapmap]
rs6114142	0.84[JPT][hapmap]
rs6114144	0.84[JPT][hapmap]
rs6132599	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132610	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132621	0.85[JPT][hapmap]
rs6132622	0.85[JPT][hapmap]
rs6132623	0.85[JPT][hapmap]
rs6132631	0.81[JPT][hapmap]
rs6137901	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6137929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137948	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6137957	0.85[JPT][hapmap]
rs6137959	0.85[JPT][hapmap]
rs6137961	0.85[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.86[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8183135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6137927	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
4	chr20:23351200-23374000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:23351400-23374000	Weak transcription	Fetal Brain Male	brain
6	chr20:23352800-23376400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr20:23353000-23378200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr20:23353400-23374200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
11	chr20:23354600-23374200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr20:23354600-23375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr20:23354800-23373600	Weak transcription	Colonic Mucosa	Colon
14	chr20:23356600-23374200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr20:23358000-23373600	Weak transcription	Right Ventricle	heart
16	chr20:23358000-23374400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:23358200-23373600	Weak transcription	Brain Angular Gyrus	brain
18	chr20:23358200-23377800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:23360200-23373600	Weak transcription	NHLF	lung
20	chr20:23361200-23399600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:23362000-23372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr20:23363000-23374400	Weak transcription	Psoas Muscle	Psoas
23	chr20:23363000-23375000	Weak transcription	Fetal Heart	heart
24	chr20:23364800-23378000	Strong transcription	Primary T cells from cord blood	blood
25	chr20:23365400-23376200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:23365600-23372600	Weak transcription	Gastric	stomach
27	chr20:23365600-23373200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:23365800-23376000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:23366000-23372800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr20:23366400-23377600	Weak transcription	Right Atrium	heart
31	chr20:23366800-23376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr20:23366800-23382400	Strong transcription	Dnd41	blood
33	chr20:23367000-23377000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:23367000-23378200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:23367200-23376000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr20:23367200-23376000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:23367200-23377600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:23367400-23373400	Weak transcription	Brain Hippocampus Middle	brain
39	chr20:23367600-23376400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr20:23367800-23376000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:23367800-23380400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr20:23368000-23373400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr20:23368000-23376200	Strong transcription	Fetal Intestine Large	intestine
44	chr20:23368000-23376400	Strong transcription	Liver	Liver
45	chr20:23368200-23375400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:23368200-23376200	Strong transcription	HepG2	liver
47	chr20:23368400-23375800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr20:23368400-23376200	Strong transcription	Brain Anterior Caudate	brain
49	chr20:23368400-23376200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:23368400-23376600	Strong transcription	Fetal Muscle Trunk	muscle

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