Variant report

Variant	rs2295238
Chromosome Location	chr20:23387946-23387947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23387020..23389665-chr20:23401490..23404499,3	MCF-7	breast:
2	chr20:23353199..23355193-chr20:23386850..23388547,2	K562	blood:
3	chr20:23381253..23384525-chr20:23386281..23388219,3	K562	blood:
4	chr20:23341861..23344169-chr20:23387452..23389386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125812	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12625160	0.89[JPT][hapmap]
rs12625164	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]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.89[JPT][hapmap]
rs1419008	1.00[LWK][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];0.85[ASN][1000 genomes]
rs17757442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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];0.85[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1984279	0.88[LWK][hapmap]
rs2277765	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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];1.00[ASN][1000 genomes]
rs2281434	1.00[CEU][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];0.92[ASN][1000 genomes]
rs3736755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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];0.85[ASN][1000 genomes]
rs3827086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55851398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56094936	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56334525	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036423	0.84[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[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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];0.94[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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];0.90[ASN][1000 genomes]
rs6132609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132610	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6132621	0.89[JPT][hapmap]
rs6132622	0.89[JPT][hapmap]
rs6132623	0.89[JPT][hapmap]
rs6132631	0.84[JPT][hapmap]
rs6137901	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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];0.85[ASN][1000 genomes]
rs6137913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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];0.85[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];0.92[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];0.92[ASN][1000 genomes]
rs6137927	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]
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];0.97[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];0.97[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];0.97[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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];0.88[ASN][1000 genomes]
rs6137948	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137957	0.89[JPT][hapmap]
rs6137959	0.89[JPT][hapmap]
rs6137961	0.89[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.86[CEU][hapmap];0.82[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
rs2295238	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 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	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
4	chr20:23361200-23399600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:23372800-23400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23375000-23389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:23375600-23390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:23375600-23396800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:23375600-23400000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:23375800-23388200	Weak transcription	Small Intestine	intestine
11	chr20:23375800-23388600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr20:23375800-23396200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:23375800-23400000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr20:23375800-23400200	Weak transcription	Fetal Brain Male	brain
15	chr20:23376000-23388600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:23376000-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr20:23376000-23390400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr20:23376200-23389000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr20:23376600-23400400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr20:23376800-23391800	Weak transcription	Adipose Nuclei	Adipose
21	chr20:23377000-23398400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr20:23378200-23388200	Weak transcription	Brain Anterior Caudate	brain
23	chr20:23378200-23391800	Weak transcription	Brain Angular Gyrus	brain
24	chr20:23378200-23400000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:23378400-23399800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr20:23378800-23390400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:23378800-23391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:23378800-23396400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr20:23378800-23399800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr20:23379000-23389600	Weak transcription	Brain Hippocampus Middle	brain
31	chr20:23379000-23400000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:23379000-23400200	Weak transcription	Primary B cells from cord blood	blood
33	chr20:23379000-23400400	Weak transcription	Brain Substantia Nigra	brain
34	chr20:23379200-23392600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr20:23379200-23400000	Weak transcription	HUVEC	blood vessel
36	chr20:23379200-23400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr20:23380400-23388200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:23380400-23388600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr20:23380800-23388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr20:23380800-23400000	Weak transcription	NH-A	brain
41	chr20:23381000-23388800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr20:23382000-23391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr20:23382000-23400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:23382200-23390600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr20:23382200-23390800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr20:23382200-23391800	Weak transcription	HSMM	muscle
47	chr20:23382200-23398400	Weak transcription	Fetal Brain Female	brain
48	chr20:23382200-23400200	Weak transcription	A549	lung
49	chr20:23382400-23392800	Weak transcription	Pancreas	Pancrea
50	chr20:23382400-23397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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