Variant report

Variant	rs12625164
Chromosome Location	chr20:23354269-23354270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23353228..23356304-chr20:23359141..23363057,4	MCF-7	breast:
2	chr20:23347716..23351207-chr20:23351737..23356214,4	MCF-7	breast:
3	chr20:23353199..23355193-chr20:23386850..23388547,2	K562	blood:
4	chr20:23353692..23356037-chr20:23360143..23361741,2	K562	blood:
5	chr20:23348293..23350635-chr20:23352571..23354458,2	K562	blood:

Variant related genes	Relation type
ENSG00000125812	Chromatin interaction
ENSG00000201728	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12625160	0.84[JPT][hapmap]
rs12625999	0.84[JPT][hapmap]
rs12626013	0.84[JPT][hapmap]
rs1419008	1.00[LWK][hapmap]
rs17757228	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]
rs17757442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17830281	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]
rs1936011	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1984279	0.90[LWK][hapmap]
rs2277765	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2281428	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];0.84[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34648279	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3736755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3746733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3761274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827086	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55851398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56094936	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs56334525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048803	0.84[JPT][hapmap]
rs6114094	0.84[JPT][hapmap]
rs6132599	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132610	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.88[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];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137910	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]
rs6137913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137927	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]
rs6137929	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]
rs6137930	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]
rs6137931	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]
rs6137936	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];0.85[ASN][1000 genomes]
rs6137937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137941	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6137948	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6137950	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6137957	0.84[JPT][hapmap]
rs6137959	0.84[JPT][hapmap]
rs6137961	0.84[JPT][hapmap]
rs761722	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8183135	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];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12625164	NXT1	cis	multi-tissue	Pritchard
rs12625164	NXT1	cis	lymphoblastoid	seeQTL

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	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
4	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:23346800-23362600	Weak transcription	Right Atrium	heart
8	chr20:23347200-23362400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr20:23347400-23362000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr20:23347600-23355200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr20:23347600-23358600	Strong transcription	Primary T cells from cord blood	blood
12	chr20:23347800-23362000	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr20:23347800-23362200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr20:23347800-23362600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:23348200-23354600	Strong transcription	Primary B cells from cord blood	blood
17	chr20:23348200-23354800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
19	chr20:23348400-23358200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr20:23348400-23362000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:23348600-23358800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr20:23348600-23362400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr20:23348600-23363000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr20:23348800-23354400	Strong transcription	HUVEC	blood vessel
25	chr20:23348800-23358000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:23348800-23358200	Strong transcription	NH-A	brain
27	chr20:23348800-23362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:23348800-23363000	Strong transcription	GM12878-XiMat	blood
29	chr20:23348800-23366400	Strong transcription	Dnd41	blood
30	chr20:23349000-23354800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr20:23349000-23354800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:23349000-23358800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:23349200-23354600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr20:23349200-23359000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:23349200-23359000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr20:23349200-23359200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr20:23349200-23359400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr20:23349200-23360400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr20:23349200-23363000	Strong transcription	Adipose Nuclei	Adipose
40	chr20:23349400-23354800	Strong transcription	Thymus	Thymus
41	chr20:23349400-23354800	Strong transcription	HMEC	breast
42	chr20:23349400-23358000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr20:23349400-23358000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr20:23349400-23358200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr20:23349400-23358200	Strong transcription	Fetal Brain Female	brain
46	chr20:23349400-23358200	Strong transcription	Fetal Intestine Large	intestine
47	chr20:23349400-23358800	Strong transcription	Left Ventricle	heart
48	chr20:23349400-23359000	Strong transcription	Fetal Muscle Leg	muscle
49	chr20:23349400-23363200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr20:23349600-23354400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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