Variant report

Variant	rs2542585
Chromosome Location	chr2:54013544-54013545
allele	C/T
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	chr2:54013517-54014999	Hela-S3	cervix:	n/a	n/a
2	REST	chr2:54013277-54015089	H1-neurons	neurons:	n/a	n/a
3	CHD1	chr2:54013399-54014361	GM12878	blood:	n/a	n/a
4	RCOR1	chr2:54013349-54014438	K562	blood:	n/a	n/a
5	ZBTB33	chr2:54013499-54014430	SK-N-SH	brain:	n/a	n/a
6	CHD2	chr2:54013514-54014524	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:54013384-54015113	Hela-S3	cervix:	n/a	n/a
8	MAX	chr2:54013544-54013545	GM12878	blood:	n/a	n/a
9	YY1	chr2:54013383-54014424	GM12891	blood:	n/a	chr2:54013780-54013790 chr2:54013564-54013572
10	MAX	chr2:54013442-54015420	Hela-S3	cervix:	n/a	n/a
11	GABPA	chr2:54013450-54014856	A549	lung:	n/a	chr2:54014079-54014088
12	SIX5	chr2:54013490-54014491	A549	lung:	n/a	n/a
13	POLR2A	chr2:54013408-54014594	K562	blood:	n/a	n/a
14	MXI1	chr2:54013208-54015472	IMR90	lung:	n/a	n/a
15	POLR2A	chr2:54013427-54014597	GM18505	blood:	n/a	n/a
16	POLR2A	chr2:54013413-54014891	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr2:54013422-54014636	K562	blood:	n/a	n/a
18	MAZ	chr2:54012927-54015605	IMR90	lung:	n/a	chr2:54013359-54013367
19	ZC3H11A	chr2:54013466-54014042	K562	blood:	n/a	n/a
20	MXI1	chr2:54013439-54015410	HepG2	liver:	n/a	n/a
21	YY1	chr2:54013407-54014353	SK-N-SH_RA	brain:	n/a	chr2:54013780-54013790 chr2:54013564-54013572
22	MAZ	chr2:54013489-54014841	K562	blood:	n/a	n/a
23	TCF12	chr2:54013367-54014955	A549	lung:	n/a	n/a
24	POLR2A	chr2:54013342-54014661	GM12892	blood:	n/a	n/a
25	BHLHE40	chr2:54013480-54014315	HepG2	liver:	n/a	chr2:54013931-54013947
26	E2F4	chr2:54013525-54014344	K562	blood:	n/a	chr2:54013699-54013713 chr2:54013702-54013709 chr2:54013702-54013709 chr2:54013702-54013709
27	POLR2A	chr2:54013509-54014759	K562	blood:	n/a	n/a
28	GTF2F1	chr2:54013445-54015193	Hela-S3	cervix:	n/a	n/a
29	MAZ	chr2:54013427-54014412	Hela-S3	cervix:	n/a	n/a
30	HEY1	chr2:54013495-54014565	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:54013442-54015119	HL-60	blood:	n/a	n/a
32	CEBPB	chr2:54013162-54014268	GM12878	blood:	n/a	n/a
33	YY1	chr2:54013388-54014572	GM12878	blood:	n/a	chr2:54013780-54013790 chr2:54013564-54013572
34	SIN3A	chr2:54013378-54014918	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:54013302-54014592	GM12892	blood:	n/a	n/a
36	EP300	chr2:54013496-54014402	K562	blood:	n/a	n/a
37	GATA3	chr2:54013506-54013802	T-47D	breast:	n/a	chr2:54013688-54013696 chr2:54013687-54013696
38	POLR2A	chr2:54013323-54013634	GM12891	blood:	n/a	n/a
39	POLR2A	chr2:54013478-54013577	MCF10A-Er-Src	breast:	n/a	n/a
40	YY1	chr2:54013432-54013764	GM12891	blood:	n/a	chr2:54013564-54013572
41	POLR2A	chr2:54013414-54014705	GM12891	blood:	n/a	n/a
42	TEAD4	chr2:54013445-54014375	K562	blood:	n/a	n/a
43	POLR2A	chr2:54013432-54014558	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:54013420-54014657	GM12878	blood:	n/a	n/a
45	WRNIP1	chr2:54013448-54014121	GM12878	blood:	n/a	n/a
46	RUNX3	chr2:54013191-54014488	GM12878	blood:	n/a	n/a
47	GATA2	chr2:54013537-54014272	SH-SY5Y	brain:	n/a	chr2:54013686-54013700 chr2:54013687-54013696
48	POLR2A	chr2:54013513-54014619	U87	brain:	n/a	n/a
49	YY1	chr2:54013425-54014145	GM12892	blood:	n/a	chr2:54013780-54013790 chr2:54013564-54013572
50	MAX	chr2:54013451-54014565	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
2	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:
3	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:

Variant related genes	Relation type
ERLEC1	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000143942	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10171954	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10178643	0.86[ASN][1000 genomes]
rs10181460	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10192626	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201938	0.87[ASN][1000 genomes]
rs10203095	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10490471	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11684084	0.82[ASN][1000 genomes]
rs12621225	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs13414216	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13417926	0.82[ASN][1000 genomes]
rs13432632	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2111623	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160929	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2160931	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs2193682	0.80[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2193683	0.82[ASN][1000 genomes]
rs2357693	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542574	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542576	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2542579	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2542584	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542588	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542593	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692515	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692518	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692531	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692532	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692537	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909263	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949811	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821081	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4413193	0.84[ASN][1000 genomes]
rs4671529	0.90[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs56173218	0.85[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs6708095	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6738369	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6743627	0.85[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs698854	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7556791	0.81[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs7557799	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7557898	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs7572776	0.88[ASN][1000 genomes]
rs7573991	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7596349	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7601692	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs805322	0.87[TSI][hapmap]
rs805373	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs805374	0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs805375	0.90[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs805410	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs805423	0.81[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs805433	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805436	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs805438	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805439	0.80[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805441	0.80[AMR][1000 genomes]
rs805450	0.88[MEX][hapmap];0.86[TSI][hapmap]
rs918207	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2542585	ACYP2	cis	Muscle Skeletal	GTEx
rs2542585	PRDXDD1P	cis	parietal	SCAN
rs2542585	PSME4	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54011600-54014000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:54011800-54015800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:54012200-54013600	Active TSS	Brain Germinal Matrix	brain
4	chr2:54012200-54014800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:54012200-54015000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:54012200-54015800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54012200-54015800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:54012400-54013600	Flanking Active TSS	Osteobl	bone
9	chr2:54012400-54014800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:54012400-54015400	Active TSS	Hela-S3	cervix
11	chr2:54012400-54015600	Active TSS	GM12878-XiMat	blood
12	chr2:54012400-54015800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:54012400-54015800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:54012400-54015800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:54012400-54016000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:54012600-54013600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54012600-54013600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:54012600-54013600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr2:54012600-54013800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:54012600-54013800	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr2:54012600-54013800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:54012600-54015200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:54012600-54015200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:54012600-54015400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:54012600-54015400	Active TSS	Fetal Kidney	kidney
26	chr2:54012600-54015400	Active TSS	NHDF-Ad	bronchial
27	chr2:54012600-54015600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:54012600-54015600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr2:54012600-54015600	Active TSS	Colonic Mucosa	Colon
30	chr2:54012600-54015600	Active TSS	K562	blood
31	chr2:54012600-54015800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:54012600-54015800	Active TSS	NHLF	lung
33	chr2:54012800-54013600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr2:54012800-54013600	Flanking Active TSS	Liver	Liver
35	chr2:54012800-54013600	Active TSS	Fetal Brain Female	brain
36	chr2:54012800-54013600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr2:54012800-54014600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:54012800-54014800	Active TSS	Brain Angular Gyrus	brain
39	chr2:54012800-54015000	Active TSS	Brain Substantia Nigra	brain
40	chr2:54012800-54015000	Active TSS	Colon Smooth Muscle	Colon
41	chr2:54012800-54015200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:54012800-54015200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr2:54012800-54015200	Active TSS	Ovary	ovary
44	chr2:54012800-54015400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:54012800-54015400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54012800-54015400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:54012800-54015600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr2:54013000-54013600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr2:54013000-54013600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:54013000-54013600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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