Variant report

Variant	rs26536
Chromosome Location	chr5:115176589-115176590
allele	A/C/G/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	MYC	chr5:115176465-115178356	A549	lung:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
3	POLR2A	chr5:115176486-115176707	MCF10A-Er-Src	breast:	n/a	n/a
4	HCFC1	chr5:115176588-115178129	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr5:115176500-115178855	IMR90	lung:	n/a	chr5:115177631-115177641 chr5:115178002-115178010
6	REST	chr5:115176576-115178512	H1-neurons	neurons:	n/a	chr5:115177983-115177996 chr5:115177983-115177996
7	MXI1	chr5:115176273-115179071	IMR90	lung:	n/a	n/a
8	POLR2A	chr5:115176149-115179154	HCT-116	colon:	n/a	n/a
9	TBP	chr5:115176147-115176649	K562	blood:	n/a	n/a
10	MXI1	chr5:115176543-115179278	SK-N-SH	brain:	n/a	n/a
11	GABPA	chr5:115176518-115177735	MCF-7	breast:	n/a	chr5:115177545-115177552 chr5:115177611-115177620
12	SP1	chr5:115176484-115178201	HCT-116	colon:	n/a	chr5:115177592-115177605 chr5:115177576-115177585 chr5:115177954-115177964 chr5:115177576-115177590 chr5:115177576-115177585 chr5:115177575-115177587 chr5:115177576-115177586 chr5:115177565-115177574 chr5:115177575-115177587 chr5:115177590-115177599 chr5:115177566-115177575 chr5:115177576-115177586 chr5:115177577-115177586
13	ELK1	chr5:115176513-115176615	GM12878	blood:	n/a	n/a
14	CHD1	chr5:115176446-115177586	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:114878345..114880939-chr5:115175674..115177985,2	K562	blood:
2	chr5:114965121..114972183-chr5:115175398..115178697,8	MCF-7	breast:
3	chr5:115169299..115172365-chr5:115175271..115177908,3	MCF-7	breast:
4	chr5:114961758..114963636-chr5:115175834..115179975,3	K562	blood:
5	chr5:114961103..114964725-chr5:115175944..115179319,4	K562	blood:
6	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:
7	chr5:115149403..115152060-chr5:115175796..115178394,2	MCF-7	breast:
8	chr20:45985552..45988522-chr5:115176582..115178558,2	MCF-7	breast:
9	chr5:115166966..115169397-chr5:115175581..115178128,2	MCF-7	breast:
10	chr5:114959625..114963439-chr5:115175786..115178902,4	MCF-7	breast:
11	chr5:115175649..115178515-chr5:115418843..115420963,3	K562	blood:
12	chr5:114951313..114954001-chr5:115175629..115177171,2	MCF-7	breast:
13	chr5:114968611..114971610-chr5:115175867..115178509,3	MCF-7	breast:

Variant related genes	Relation type
AP3S1	TF binding region
ATG12	TF binding region
ENSG00000134970	Chromatin interaction
ENSG00000251201	Chromatin interaction
ENSG00000145781	Chromatin interaction
ENSG00000145782	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000129596	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10039749	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10434761	0.91[ASN][1000 genomes]
rs1058600	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs10751460	0.83[ASN][1000 genomes]
rs11241336	0.85[ASN][1000 genomes]
rs11241337	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12188972	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12332653	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12513891	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12514553	0.84[ASN][1000 genomes]
rs12517882	0.85[ASN][1000 genomes]
rs12520248	0.91[ASN][1000 genomes]
rs12521324	0.82[ASN][1000 genomes]
rs13157716	0.85[ASN][1000 genomes]
rs13174348	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs13179199	0.82[ASN][1000 genomes]
rs13361489	0.81[ASN][1000 genomes]
rs152368	0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs152369	0.85[ASN][1000 genomes]
rs152397	0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs152398	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs154757	0.88[ASN][1000 genomes]
rs154759	0.81[ASN][1000 genomes]
rs171809	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2080902	0.85[ASN][1000 genomes]
rs26529	0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs26531	0.81[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26533	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26534	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26535	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26537	0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs26538	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]
rs34850	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs34851	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34852	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34869	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs35053218	0.85[ASN][1000 genomes]
rs35179959	0.94[ASN][1000 genomes]
rs35238578	0.81[ASN][1000 genomes]
rs35501287	0.86[ASN][1000 genomes]
rs35903246	0.92[ASN][1000 genomes]
rs3797567	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3797568	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3797569	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3797570	0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs40095	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41332950	0.86[JPT][hapmap]
rs4143542	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs57633641	0.94[ASN][1000 genomes]
rs59750231	0.85[ASN][1000 genomes]
rs61381571	0.86[ASN][1000 genomes]
rs6594906	0.94[ASN][1000 genomes]
rs6872406	0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6879485	0.83[ASN][1000 genomes]
rs6880889	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7707539	0.83[ASN][1000 genomes]
rs7713314	0.86[ASN][1000 genomes]
rs7726368	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26536	ENSG00000145782	cis	multi-tissue	Pritchard
rs26536	ATG12	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115162000-115176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:115174200-115176600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:115174200-115176600	Flanking Active TSS	Dnd41	blood
4	chr5:115174400-115176600	Flanking Active TSS	Liver	Liver
5	chr5:115174400-115176600	Flanking Active TSS	HUVEC	blood vessel
6	chr5:115174600-115180000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:115174800-115178600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:115175000-115176600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr5:115175000-115176800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr5:115175000-115178200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:115175000-115178800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:115175200-115176800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:115175200-115177000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr5:115175200-115178200	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr5:115175200-115178400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:115175400-115177000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:115175400-115178200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr5:115175400-115178400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:115175400-115178800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:115175600-115176600	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr5:115175600-115176800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr5:115175600-115178000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:115175600-115178800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:115175600-115179000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:115175600-115179000	Active TSS	Placenta	Placenta
26	chr5:115175600-115179200	Active TSS	Right Ventricle	heart
27	chr5:115175600-115179400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:115175600-115180000	Active TSS	Stomach Smooth Muscle	stomach
29	chr5:115175600-115180200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:115175800-115176600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:115175800-115176600	Enhancers	Spleen	Spleen
32	chr5:115175800-115178200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr5:115175800-115178600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:115175800-115178800	Active TSS	A549	lung
35	chr5:115175800-115178800	Active TSS	HSMM	muscle
36	chr5:115175800-115179000	Active TSS	Psoas Muscle	Psoas
37	chr5:115175800-115179000	Active TSS	NHDF-Ad	bronchial
38	chr5:115175800-115179600	Active TSS	Ovary	ovary
39	chr5:115176000-115176600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:115176000-115176600	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr5:115176000-115176600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr5:115176000-115177800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:115176000-115178600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:115176000-115178600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:115176000-115178600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:115176000-115178600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr5:115176000-115178600	Active TSS	Fetal Intestine Small	intestine
48	chr5:115176000-115178600	Active TSS	K562	blood
49	chr5:115176000-115178800	Active TSS	Fetal Intestine Large	intestine
50	chr5:115176000-115178800	Active TSS	Rectal Smooth Muscle	rectum

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