Variant report

Variant	rs26538
Chromosome Location	chr5:115178395-115178396
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	chr5:115176349-115179027	GM12891	blood:	n/a	n/a
2	EP300	chr5:115178180-115178475	GM12878	blood:	n/a	n/a
3	BHLHE40	chr5:115177026-115178548	K562	blood:	n/a	chr5:115177614-115177630
4	MYC	chr5:115176953-115178540	NB4	blood:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
5	MAX	chr5:115177034-115178490	NB4	blood:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
6	SMARCC1	chr5:115176611-115178396	Hela-S3	cervix:	n/a	n/a
7	MYC	chr5:115176832-115178452	K562	blood:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
8	SMC3	chr5:115178243-115178441	GM12878	blood:	n/a	n/a
9	MAZ	chr5:115176985-115178569	GM12878	blood:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
10	WRNIP1	chr5:115178187-115178411	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:115176963-115178472	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:115176866-115178442	GM18526	blood:	n/a	n/a
13	GATA2	chr5:115177031-115178420	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr5:115176907-115178402	GM19193	blood:	n/a	n/a
15	MAX	chr5:115176992-115178454	K562	blood:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
16	HA-E2F1	chr5:115176846-115178491	MCF-7	breast:	n/a	chr5:115177572-115177582 chr5:115177812-115177822
17	MAZ	chr5:115176500-115178855	IMR90	lung:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
18	JUND	chr5:115177030-115178558	K562	blood:	n/a	n/a
19	REST	chr5:115176576-115178512	H1-neurons	neurons:	n/a	chr5:115177983-115177996 chr5:115177983-115177996
20	MXI1	chr5:115177032-115178505	HepG2	liver:	n/a	n/a
21	EP300	chr5:115178265-115178465	GM12878	blood:	n/a	n/a
22	KAP1	chr5:115177885-115178982	HEK293	kidney:	n/a	n/a
23	ZNF143	chr5:115177054-115178446	GM12878	blood:	n/a	chr5:115177562-115177580
24	MXI1	chr5:115176273-115179071	IMR90	lung:	n/a	n/a
25	MAX	chr5:115176916-115178558	HepG2	liver:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
26	ZBTB7A	chr5:115177096-115178417	ECC-1	luminal epithelium:	n/a	chr5:115177580-115177587
27	SIN3A	chr5:115176677-115178467	GM12878	blood:	n/a	chr5:115177849-115177862 chr5:115177976-115177987
28	RUNX3	chr5:115178168-115178590	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:115176149-115179154	HCT-116	colon:	n/a	n/a
30	GATA1	chr5:115176737-115179485	PBDE	blood:	n/a	chr5:115178735-115178756 chr5:115178957-115178967 chr5:115178738-115178751
31	CHD1	chr5:115176620-115178673	IMR90	lung:	n/a	chr5:115177828-115177838
32	POLR2A	chr5:115178356-115178396	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr5:115176944-115178395	PANC-1	pancreas:	n/a	n/a
34	MAX	chr5:115177031-115178571	MCF-7	breast:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
35	POLR2A	chr5:115176716-115178424	Raji	blood:	n/a	n/a
36	UBTF	chr5:115176817-115178453	K562	blood:	n/a	n/a
37	CHD2	chr5:115176924-115178527	K562	blood:	n/a	chr5:115177828-115177838
38	POLR2A	chr5:115176850-115178693	PBDE	blood:	n/a	n/a
39	MXI1	chr5:115176543-115179278	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr5:115176960-115178419	GM18505	blood:	n/a	n/a
41	POLR2A	chr5:115176838-115178442	GM18951	blood:	n/a	n/a
42	NR3C1	chr5:115178128-115178604	A549	lung:	n/a	chr5:115178285-115178292 chr5:115178276-115178294
43	POLR2A	chr5:115176889-115178445	GM19099	blood:	n/a	n/a
44	CREB1	chr5:115176946-115178418	HepG2	liver:	n/a	n/a
45	GATA2	chr5:115176990-115178470	SH-SY5Y	brain:	n/a	n/a
46	NR3C1	chr5:115178154-115178580	A549	lung:	n/a	chr5:115178285-115178292 chr5:115178276-115178294
47	MXI1	chr5:115176856-115178679	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:115178270-115178395	MCF10A-Er-Src	breast:	n/a	n/a
49	SIN3A	chr5:115176790-115178453	H1-hESC	embryonic stem cell:	n/a	chr5:115177849-115177862 chr5:115177976-115177987
50	MAX	chr5:115176881-115178565	A549	lung:	n/a	chr5:115177631-115177641 chr5:115178002-115178010

No.	Distal block	Cell Line	Cell type
1	chr5:114965121..114972183-chr5:115175398..115178697,8	MCF-7	breast:
2	chr5:114630836..114633202-chr5:115177399..115179913,2	MCF-7	breast:
3	chr5:114961758..114963636-chr5:115175834..115179975,3	K562	blood:
4	chr5:114961103..114964725-chr5:115175944..115179319,4	K562	blood:
5	chr5:115177412..115179376-chr5:115201368..115203253,2	MCF-7	breast:
6	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:
7	chr20:45985552..45988522-chr5:115176582..115178558,2	MCF-7	breast:
8	chr5:115177015..115179299-chr5:115418616..115421272,3	K562	blood:
9	chr5:114959625..114963439-chr5:115175786..115178902,4	MCF-7	breast:
10	chr5:115175649..115178515-chr5:115418843..115420963,3	K562	blood:
11	chr5:114968611..114971610-chr5:115175867..115178509,3	MCF-7	breast:
12	chr5:114950483..114953448-chr5:115177527..115180006,2	K562	blood:
13	chr5:115177392..115178980-chr5:115419410..115421076,2	MCF-7	breast:

Variant related genes	Relation type
ATG12	TF binding region
ENSG00000164221	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000145781	Chromatin interaction
ENSG00000251201	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000271918	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10039749	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10050876	0.82[ASN][1000 genomes]
rs1058600	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs10751460	0.94[ASN][1000 genomes]
rs11241336	0.96[ASN][1000 genomes]
rs11241337	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12188972	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12332653	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12513891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12514553	0.95[ASN][1000 genomes]
rs12517882	0.96[ASN][1000 genomes]
rs12519850	0.88[ASN][1000 genomes]
rs12520442	0.88[ASN][1000 genomes]
rs12523122	0.88[ASN][1000 genomes]
rs13157716	0.96[ASN][1000 genomes]
rs13179199	0.91[ASN][1000 genomes]
rs13361489	0.91[ASN][1000 genomes]
rs152368	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs152369	0.96[ASN][1000 genomes]
rs152397	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs152398	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171809	0.84[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2080902	0.96[ASN][1000 genomes]
rs26529	0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26531	0.89[CHD][hapmap]
rs26533	0.81[ASN][1000 genomes]
rs26534	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs26535	0.82[ASN][1000 genomes]
rs26536	1.00[ASW][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs26537	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35179959	0.81[ASN][1000 genomes]
rs35238578	0.90[ASN][1000 genomes]
rs35501287	0.96[ASN][1000 genomes]
rs3733902	0.86[CHB][hapmap]
rs3756555	0.85[CHB][hapmap]
rs3797564	0.81[CHB][hapmap]
rs3797565	0.88[ASN][1000 genomes]
rs3797566	0.86[CHB][hapmap]
rs3797567	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3797568	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3797569	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3797570	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs41332950	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4143542	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs57633641	0.81[ASN][1000 genomes]
rs58463583	0.82[ASN][1000 genomes]
rs59750231	0.96[ASN][1000 genomes]
rs61381571	0.96[ASN][1000 genomes]
rs6594906	0.81[ASN][1000 genomes]
rs6872406	0.86[CHD][hapmap]
rs6879485	0.93[ASN][1000 genomes]
rs6880372	0.86[ASN][1000 genomes]
rs6880889	0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs71581217	0.88[ASN][1000 genomes]
rs7707539	0.94[ASN][1000 genomes]
rs7713314	0.96[ASN][1000 genomes]
rs7726368	0.81[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	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3410990	chr5:115177597-115205832	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	esv3382194	chr5:115177673-115205801	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26538	ATG12	cis	multi-tissue	Pritchard
rs26538	ATG12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115174600-115180000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:115174800-115178600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:115175000-115178800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:115175200-115178400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:115175400-115178400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr5:115175400-115178800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:115175600-115178800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:115175600-115179000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:115175600-115179000	Active TSS	Placenta	Placenta
10	chr5:115175600-115179200	Active TSS	Right Ventricle	heart
11	chr5:115175600-115179400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:115175600-115180000	Active TSS	Stomach Smooth Muscle	stomach
13	chr5:115175600-115180200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:115175800-115178600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:115175800-115178800	Active TSS	A549	lung
16	chr5:115175800-115178800	Active TSS	HSMM	muscle
17	chr5:115175800-115179000	Active TSS	Psoas Muscle	Psoas
18	chr5:115175800-115179000	Active TSS	NHDF-Ad	bronchial
19	chr5:115175800-115179600	Active TSS	Ovary	ovary
20	chr5:115176000-115178600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:115176000-115178600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:115176000-115178600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr5:115176000-115178600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr5:115176000-115178600	Active TSS	Fetal Intestine Small	intestine
25	chr5:115176000-115178600	Active TSS	K562	blood
26	chr5:115176000-115178800	Active TSS	Fetal Intestine Large	intestine
27	chr5:115176000-115178800	Active TSS	Rectal Smooth Muscle	rectum
28	chr5:115176000-115178800	Active TSS	NHEK	skin
29	chr5:115176000-115179000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr5:115176000-115179000	Active TSS	HSMMtube	muscle
31	chr5:115176000-115179200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:115176000-115179600	Active TSS	GM12878-XiMat	blood
33	chr5:115176000-115180200	Active TSS	Right Atrium	heart
34	chr5:115176200-115178600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr5:115176200-115178600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:115176200-115178600	Active TSS	Fetal Kidney	kidney
37	chr5:115176200-115178600	Active TSS	Lung	lung
38	chr5:115176200-115178600	Active TSS	Stomach Mucosa	stomach
39	chr5:115176200-115178800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:115176200-115178800	Active TSS	Pancreas	Pancrea
41	chr5:115176200-115179200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr5:115176400-115178400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:115176400-115178400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:115176400-115178600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:115176400-115178600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr5:115176400-115178600	Active TSS	Colon Smooth Muscle	Colon
47	chr5:115176400-115178600	Active TSS	Duodenum Mucosa	Duodenum
48	chr5:115176400-115178600	Active TSS	Esophagus	oesophagus
49	chr5:115176400-115178600	Active TSS	Fetal Lung	lung
50	chr5:115176400-115178600	Active TSS	Gastric	stomach

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