Variant report

Variant	rs26534
Chromosome Location	chr5:115175701-115175702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:115174673-115176061	A549	lung:	n/a	n/a
2	POLR2A	chr5:115174756-115176043	HCT-116	colon:	n/a	n/a

No data

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

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	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:
5	chr5:115166966..115169397-chr5:115175581..115178128,2	MCF-7	breast:
6	chr5:115175649..115178515-chr5:115418843..115420963,3	K562	blood:
7	chr5:114951313..114954001-chr5:115175629..115177171,2	MCF-7	breast:

No data

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

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10434761	0.93[ASN][1000 genomes]
rs1058600	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs11241336	0.81[ASN][1000 genomes]
rs12188972	0.81[CHD][hapmap]
rs12189155	0.81[ASN][1000 genomes]
rs12514553	0.80[ASN][1000 genomes]
rs12517882	0.81[ASN][1000 genomes]
rs12520248	0.93[ASN][1000 genomes]
rs12521324	0.83[ASN][1000 genomes]
rs13157716	0.81[ASN][1000 genomes]
rs13174348	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs152368	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs152369	0.81[ASN][1000 genomes]
rs152397	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs152398	0.83[ASN][1000 genomes]
rs154757	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154759	0.83[ASN][1000 genomes]
rs171809	0.84[CHD][hapmap]
rs2080902	0.81[ASN][1000 genomes]
rs26529	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs26531	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs26533	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26535	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26536	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]
rs26537	0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs26538	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs34850	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34851	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34852	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34869	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs35053218	0.87[ASN][1000 genomes]
rs35179959	0.96[ASN][1000 genomes]
rs35501287	0.81[ASN][1000 genomes]
rs35903246	0.93[ASN][1000 genomes]
rs3797568	0.81[CHD][hapmap]
rs3797569	0.89[CHD][hapmap]
rs3797570	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs40095	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143542	0.81[CHD][hapmap]
rs57633641	0.97[ASN][1000 genomes]
rs59750231	0.81[ASN][1000 genomes]
rs61381571	0.81[ASN][1000 genomes]
rs6594906	0.97[ASN][1000 genomes]
rs6872406	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6880889	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs7713314	0.81[ASN][1000 genomes]
rs7726368	0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs26534	FEM1C	cis	lymphoblastoid	seeQTL
rs26534	ATG12	cis	cerebellum	SCAN
rs26534	ATG12	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115161800-115176200	Weak transcription	Gastric	stomach
2	chr5:115162000-115176200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:115162000-115176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:115163000-115176400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:115168400-115176400	Weak transcription	Aorta	Aorta
6	chr5:115173400-115176200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:115173400-115176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:115173800-115176200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:115174000-115175800	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:115174000-115176000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:115174000-115176000	Enhancers	Stomach Mucosa	stomach
12	chr5:115174000-115176000	Flanking Active TSS	HepG2	liver
13	chr5:115174000-115176200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr5:115174000-115176200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:115174000-115176200	Enhancers	Brain Substantia Nigra	brain
16	chr5:115174000-115176200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:115174200-115175800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:115174200-115176200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr5:115174200-115176200	Genic enhancers	Primary B cells from cord blood	blood
20	chr5:115174200-115176200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr5:115174200-115176600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:115174200-115176600	Flanking Active TSS	Dnd41	blood
23	chr5:115174400-115176000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr5:115174400-115176000	Enhancers	Rectal Smooth Muscle	rectum
25	chr5:115174400-115176000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr5:115174400-115176200	Enhancers	Brain Angular Gyrus	brain
27	chr5:115174400-115176200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:115174400-115176200	Enhancers	Fetal Heart	heart
29	chr5:115174400-115176200	Enhancers	Fetal Lung	lung
30	chr5:115174400-115176200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:115174400-115176400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr5:115174400-115176600	Flanking Active TSS	Liver	Liver
33	chr5:115174400-115176600	Flanking Active TSS	HUVEC	blood vessel
34	chr5:115174600-115175800	Active TSS	Fetal Brain Female	brain
35	chr5:115174600-115175800	Enhancers	HSMM	muscle
36	chr5:115174600-115176000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr5:115174600-115176400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:115174600-115180000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:115174800-115175800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:115174800-115175800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr5:115174800-115175800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:115174800-115175800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:115174800-115175800	Enhancers	Fetal Intestine Large	intestine
44	chr5:115174800-115175800	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:115174800-115175800	Weak transcription	Left Ventricle	heart
46	chr5:115174800-115175800	Active TSS	Right Atrium	heart
47	chr5:115174800-115175800	Weak transcription	Spleen	Spleen
48	chr5:115174800-115176000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:115174800-115176000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:115174800-115176000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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