Variant report

Variant	rs1992133
Chromosome Location	chr2:73301618-73301619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73297000..73299065-chr2:73300438..73301965,2	MCF-7	breast:
2	chr2:73300909..73302911-chr2:73316133..73317647,2	K562	blood:
3	chr2:73300396..73302911-chr2:73315000..73317633,2	K562	blood:
4	chr2:73247423..73249390-chr2:73299554..73302236,2	K562	blood:

Variant related genes	Relation type
ENSG00000144040	Chromatin interaction
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10166220	0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes]
rs10167566	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10174548	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10176939	0.80[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs10177159	0.80[JPT][hapmap]
rs10178944	0.85[AMR][1000 genomes]
rs10180720	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10180995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10189744	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192077	1.00[ASW][hapmap];0.80[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10197305	0.80[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs10203608	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1036512	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1046186	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865396	0.83[ASN][1000 genomes]
rs11126389	0.83[ASN][1000 genomes]
rs11686557	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11885522	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12104691	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12233055	0.80[CEU][hapmap];0.80[JPT][hapmap];0.90[TSI][hapmap]
rs12614059	0.86[ASN][1000 genomes]
rs13018842	0.83[ASN][1000 genomes]
rs13385994	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388404	0.90[JPT][hapmap]
rs13390072	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13391532	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13393567	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13400920	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13400948	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13403757	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs13403781	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs13407719	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13416407	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13427947	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370383	0.82[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs1430349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1430350	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430351	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17008571	0.85[JPT][hapmap];0.84[YRI][hapmap]
rs17008611	0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs17008631	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2421098	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3813222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813223	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3901273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4144837	0.87[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4514897	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4591365	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55894650	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55974516	0.83[AMR][1000 genomes]
rs57536428	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57701326	0.94[ASN][1000 genomes]
rs57726945	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57937746	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61161134	0.83[AMR][1000 genomes]
rs6546796	0.82[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs6546797	0.88[ASW][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6546800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546801	0.91[ASN][1000 genomes]
rs6709938	0.85[JPT][hapmap]
rs6710739	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6711891	0.85[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs6712925	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6713655	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6719333	0.80[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs6720817	0.99[ASN][1000 genomes]
rs6726940	0.80[JPT][hapmap]
rs6727269	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6727919	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729266	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs6732369	0.80[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs6736153	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs6749237	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6750069	0.80[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs6754779	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6754858	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6757131	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs6759733	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs727470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs727471	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs732178	0.80[CEU][hapmap]
rs732179	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs732180	0.80[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs7557173	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7559074	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7566904	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7570876	0.90[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs7579770	0.85[JPT][hapmap]
rs7580216	0.80[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[TSI][hapmap]
rs7593322	0.93[ASN][1000 genomes]
rs7597032	0.85[JPT][hapmap]
rs7599657	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602651	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891432	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs891433	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs893258	0.85[JPT][hapmap]
rs893259	0.85[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs9309471	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992133	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299200-73301800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:73299200-73314800	Weak transcription	Small Intestine	intestine
3	chr2:73299400-73302000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:73299400-73302000	Weak transcription	Esophagus	oesophagus
5	chr2:73299400-73302000	Weak transcription	Ovary	ovary
6	chr2:73299400-73302200	Weak transcription	Lung	lung
7	chr2:73299400-73306800	Weak transcription	Fetal Brain Male	brain
8	chr2:73299400-73314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:73299400-73314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:73299600-73301800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:73299600-73302000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:73299600-73302000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:73299600-73302000	Weak transcription	Right Ventricle	heart
16	chr2:73299600-73302000	Weak transcription	A549	lung
17	chr2:73299600-73302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:73299600-73302200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:73299600-73302200	Weak transcription	Hela-S3	cervix
20	chr2:73299600-73302600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:73299600-73302800	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:73299600-73303000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:73299600-73305600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:73299600-73305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:73299600-73306400	Weak transcription	Brain Anterior Caudate	brain
26	chr2:73299600-73306600	Weak transcription	Brain Angular Gyrus	brain
27	chr2:73299600-73306600	Weak transcription	Left Ventricle	heart
28	chr2:73299600-73307600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:73299600-73307800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:73299600-73312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:73299600-73314200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:73299600-73314600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:73299600-73314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:73299600-73315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:73299600-73316000	Weak transcription	NHDF-Ad	bronchial
36	chr2:73299600-73319400	Weak transcription	K562	blood
37	chr2:73299800-73302000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:73299800-73302400	Weak transcription	Psoas Muscle	Psoas
39	chr2:73299800-73302400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:73299800-73307600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:73299800-73308000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:73299800-73311200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
44	chr2:73299800-73314800	Weak transcription	HSMM	muscle
45	chr2:73300000-73302000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:73300000-73302000	Weak transcription	Adipose Nuclei	Adipose
47	chr2:73300000-73302800	Weak transcription	HMEC	breast
48	chr2:73300000-73305400	Strong transcription	Osteobl	bone
49	chr2:73300000-73307800	Strong transcription	Placenta	Placenta
50	chr2:73300000-73308800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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