Variant report

Variant	rs805375
Chromosome Location	chr2:54090405-54090406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

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	TCF7L2	chr2:54090351-54090544	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:54089805-54090560	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:54089808-54090629	A549	lung:	n/a	n/a
5	POLR2A	chr2:54090302-54090702	K562	blood:	n/a	n/a
6	POLR2A	chr2:54090280-54090771	K562	blood:	n/a	n/a
7	POLR2A	chr2:54090048-54090670	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54089565..54091818-chr2:54091926..54093563,2	MCF-7	breast:
2	chr2:54084019..54085581-chr2:54090209..54092040,2	K562	blood:
3	chr2:54086141..54088584-chr2:54089355..54091721,3	K562	blood:
4	chr2:54086271..54088686-chr2:54089526..54092014,2	MCF-7	breast:

No data

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

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10084355	0.80[AMR][1000 genomes]
rs10201364	0.80[AMR][1000 genomes]
rs10203095	0.80[EUR][1000 genomes]
rs11683654	0.80[CHB][hapmap]
rs13414393	0.86[GIH][hapmap]
rs13417926	0.85[EUR][1000 genomes]
rs13432632	0.89[CEU][hapmap]
rs1363062	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs1363063	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1421617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs17045439	0.91[JPT][hapmap]
rs2111623	0.92[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2111868	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2160931	0.89[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs2302878	0.91[JPT][hapmap]
rs2357693	0.92[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.93[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	0.90[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2542588	0.90[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2692518	0.88[EUR][1000 genomes]
rs2884254	0.81[AMR][1000 genomes]
rs2909460	0.81[AMR][1000 genomes]
rs3821081	0.89[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs6708095	0.92[CEU][hapmap]
rs6738369	0.80[EUR][1000 genomes]
rs6743627	0.87[TSI][hapmap]
rs6749817	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs698854	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs698858	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs718872	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7557898	0.87[TSI][hapmap]
rs7558126	0.87[CHB][hapmap]
rs7569214	0.81[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs7569370	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7596349	0.95[CEU][hapmap]
rs7601692	0.85[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs805308	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805309	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs805317	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs805318	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs805320	0.90[ASN][1000 genomes]
rs805322	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs805330	0.89[ASN][1000 genomes]
rs805341	0.81[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap]
rs805345	0.80[AMR][1000 genomes]
rs805358	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs805359	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs805360	0.87[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs805361	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs805366	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs805367	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805373	0.81[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs805374	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	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805380	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805391	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805392	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805393	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805396	0.83[AMR][1000 genomes]
rs805402	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805405	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805410	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs805412	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs805421	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805422	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs805423	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805424	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs805430	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs805433	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805436	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs805438	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs805439	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805441	0.86[EUR][1000 genomes]
rs805444	0.81[EUR][1000 genomes]
rs805450	0.87[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs805453	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs809280	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs805375	C2orf73	cis	cerebellum	SCAN
rs805375	ACYP2	cis	Muscle Skeletal	GTEx

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	chr2:54081800-54092200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:54081800-54094400	Weak transcription	Small Intestine	intestine
12	chr2:54082000-54091000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:54082000-54091200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:54082000-54091200	Weak transcription	Placenta	Placenta
15	chr2:54082000-54092000	Weak transcription	GM12878-XiMat	blood
16	chr2:54082200-54090800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:54082800-54093800	Weak transcription	Spleen	Spleen
18	chr2:54083800-54091200	Weak transcription	Dnd41	blood
19	chr2:54083800-54092800	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:54084000-54102000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:54084200-54093200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:54085400-54106600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:54086600-54101200	Weak transcription	Fetal Brain Male	brain
24	chr2:54087000-54168000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:54087400-54090600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:54087400-54090600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:54087400-54091800	Weak transcription	NHDF-Ad	bronchial
29	chr2:54087400-54092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54087400-54092000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:54087400-54092400	Weak transcription	Gastric	stomach
32	chr2:54087400-54093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:54087400-54097400	Strong transcription	Primary B cells from cord blood	blood
34	chr2:54087400-54112200	Weak transcription	Psoas Muscle	Psoas
35	chr2:54087400-54112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:54087400-54117400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:54087400-54137600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:54087600-54090600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:54087600-54090600	Weak transcription	Fetal Stomach	stomach
40	chr2:54087600-54090800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:54087600-54091000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:54087600-54091000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:54087600-54091000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:54087600-54091200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54087600-54091200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:54087600-54091200	Weak transcription	NH-A	brain
47	chr2:54087600-54091200	Weak transcription	NHLF	lung
48	chr2:54087600-54091800	Weak transcription	Fetal Lung	lung
49	chr2:54087600-54092000	Weak transcription	Aorta	Aorta
50	chr2:54087600-54092000	Weak transcription	Thymus	Thymus

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