Variant report

Variant	rs805374
Chromosome Location	chr2:54089857-54089858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54085702-54091507	K562	blood:	n/a	n/a
2	POLR2A	chr2:54089792-54089998	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:54089746-54090049	K562	blood:	n/a	n/a
4	POLR2A	chr2:54089802-54089936	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:54089805-54090560	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:54089808-54090629	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54089565..54091818-chr2:54091926..54093563,2	MCF-7	breast:
2	chr2:54086141..54088584-chr2:54089355..54091721,3	K562	blood:
3	chr2:54086271..54088686-chr2:54089526..54092014,2	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
GPR75	TF binding region
ENSG00000270898	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000270898	Chromatin interaction
ENSG00000119737	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10203095	0.80[EUR][1000 genomes]
rs10203576	0.80[AMR][1000 genomes]
rs11683654	0.86[CHB][hapmap]
rs13414393	0.83[GIH][hapmap]
rs13417926	0.85[EUR][1000 genomes]
rs13432632	0.89[CEU][hapmap]
rs1363062	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1363063	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1421617	0.81[CEU][hapmap];0.93[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs1421622	0.80[AMR][1000 genomes]
rs17045439	0.91[JPT][hapmap]
rs2111623	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2111868	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2160931	0.89[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs2302878	0.91[JPT][hapmap]
rs2357693	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2542574	0.89[EUR][1000 genomes]
rs2542576	0.90[EUR][1000 genomes]
rs2542579	0.85[EUR][1000 genomes]
rs2542585	0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2542588	0.88[GIH][hapmap]
rs2692518	0.88[EUR][1000 genomes]
rs2884254	0.80[AMR][1000 genomes]
rs3821081	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs6708095	0.92[CEU][hapmap]
rs6738369	0.80[EUR][1000 genomes]
rs6743627	0.85[TSI][hapmap]
rs6749817	0.92[CHB][hapmap]
rs698854	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs698858	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs718872	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7557898	0.85[TSI][hapmap]
rs7558126	0.80[CHB][hapmap]
rs7569214	0.81[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap]
rs7569370	0.81[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs7596349	0.95[CEU][hapmap]
rs7601692	0.85[CEU][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs805308	0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs805309	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs805317	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs805318	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs805320	0.90[ASN][1000 genomes]
rs805322	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805330	0.88[ASN][1000 genomes]
rs805341	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs805358	0.84[ASN][1000 genomes]
rs805359	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805360	0.93[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs805361	0.84[ASN][1000 genomes]
rs805366	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs805367	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805373	0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs805375	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805379	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805380	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805391	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805392	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805393	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805396	0.83[AMR][1000 genomes]
rs805402	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805405	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805410	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs805421	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805422	0.94[ASN][1000 genomes]
rs805423	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805424	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805430	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs805433	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805436	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805438	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805439	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805441	0.86[EUR][1000 genomes]
rs805444	0.81[EUR][1000 genomes]
rs805450	0.89[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs805453	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs809280	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs805374	ACYP2	cis	Muscle Skeletal	GTEx
rs805374	C2orf73	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54074800-54096600	Weak transcription	Hela-S3	cervix
2	chr2:54078600-54092200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54078800-54092400	Weak transcription	K562	blood
4	chr2:54079000-54091800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:54079600-54090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:54081200-54091800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:54081600-54090600	Weak transcription	HUVEC	blood vessel
8	chr2:54081600-54091200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:54081600-54091600	Weak transcription	HSMMtube	muscle
10	chr2:54081800-54090000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:54081800-54090200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:54081800-54092200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:54081800-54094400	Weak transcription	Small Intestine	intestine
14	chr2:54082000-54090400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:54082000-54091000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:54082000-54091200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:54082000-54091200	Weak transcription	Placenta	Placenta
18	chr2:54082000-54092000	Weak transcription	GM12878-XiMat	blood
19	chr2:54082200-54090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:54082200-54090800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:54082800-54093800	Weak transcription	Spleen	Spleen
22	chr2:54083800-54091200	Weak transcription	Dnd41	blood
23	chr2:54083800-54092800	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:54084000-54102000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:54084200-54093200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:54085400-54106600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:54086600-54101200	Weak transcription	Fetal Brain Male	brain
28	chr2:54087000-54168000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:54087400-54090200	Weak transcription	HepG2	liver
31	chr2:54087400-54090400	Weak transcription	Fetal Kidney	kidney
32	chr2:54087400-54090400	Weak transcription	Lung	lung
33	chr2:54087400-54090400	Weak transcription	Right Ventricle	heart
34	chr2:54087400-54090600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:54087400-54090600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:54087400-54091800	Weak transcription	NHDF-Ad	bronchial
37	chr2:54087400-54092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:54087400-54092000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:54087400-54092400	Weak transcription	Gastric	stomach
40	chr2:54087400-54093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:54087400-54097400	Strong transcription	Primary B cells from cord blood	blood
42	chr2:54087400-54112200	Weak transcription	Psoas Muscle	Psoas
43	chr2:54087400-54112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:54087400-54117400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:54087400-54137600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:54087600-54090200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:54087600-54090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:54087600-54090200	Weak transcription	Fetal Intestine Large	intestine
49	chr2:54087600-54090400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:54087600-54090400	Weak transcription	Adipose Nuclei	Adipose

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