Variant report

Variant	rs17757228
Chromosome Location	chr20:23351288-23351289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23349924..23351887-chr20:23357780..23360381,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12625160	0.84[JPT][hapmap]
rs12625164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.84[JPT][hapmap]
rs17757442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17830281	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]
rs1936011	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277765	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281428	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];0.85[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295238	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];0.85[ASN][1000 genomes]
rs34648279	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3736755	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]
rs3746733	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]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827086	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55851398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56094936	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56334525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
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	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132610	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132621	0.84[JPT][hapmap]
rs6132622	0.84[JPT][hapmap]
rs6132623	0.84[JPT][hapmap]
rs6137901	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137910	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]
rs6137913	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]
rs6137914	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137915	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]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137927	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]
rs6137929	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]
rs6137930	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]
rs6137931	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]
rs6137936	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];0.87[ASN][1000 genomes]
rs6137937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137938	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];0.85[ASN][1000 genomes]
rs6137939	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];0.85[ASN][1000 genomes]
rs6137941	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137948	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137950	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137957	0.84[JPT][hapmap]
rs6137959	0.84[JPT][hapmap]
rs6137961	0.84[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8183135	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];0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17757228	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	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:23344600-23354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
6	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr20:23346800-23362600	Weak transcription	Right Atrium	heart
10	chr20:23347200-23362400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr20:23347400-23362000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr20:23347600-23355200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr20:23347600-23358600	Strong transcription	Primary T cells from cord blood	blood
14	chr20:23347800-23362000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr20:23347800-23362200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:23347800-23362600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:23348000-23353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr20:23348200-23351400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr20:23348200-23354600	Strong transcription	Primary B cells from cord blood	blood
21	chr20:23348200-23354800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
23	chr20:23348400-23358200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr20:23348400-23362000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr20:23348600-23351400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr20:23348600-23358800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr20:23348600-23362400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr20:23348600-23363000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr20:23348800-23352200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr20:23348800-23354200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr20:23348800-23354400	Strong transcription	HUVEC	blood vessel
32	chr20:23348800-23358000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:23348800-23358200	Strong transcription	NH-A	brain
34	chr20:23348800-23362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr20:23348800-23363000	Strong transcription	GM12878-XiMat	blood
36	chr20:23348800-23366400	Strong transcription	Dnd41	blood
37	chr20:23349000-23351600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr20:23349000-23354800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr20:23349000-23354800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr20:23349000-23358800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:23349200-23354000	Strong transcription	A549	lung
42	chr20:23349200-23354600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr20:23349200-23359000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:23349200-23359000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr20:23349200-23359200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr20:23349200-23359400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:23349200-23360400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:23349200-23363000	Strong transcription	Adipose Nuclei	Adipose
49	chr20:23349400-23351600	Strong transcription	Colonic Mucosa	Colon
50	chr20:23349400-23352000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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