Variant report

Variant	rs13239855
Chromosome Location	chr7:47985263-47985264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:47984519..47985336-chr7:48008536..48009073,2	MCF-7	breast:
2	chr7:47984965..47986938-chr7:47988162..47990314,2	K562	blood:
3	chr7:47984610..47985431-chr7:48140959..48141660,2	K562	blood:
4	chr7:47983989..47986753-chr7:48157861..48159933,2	K562	blood:
5	chr7:47984512..47985468-chr7:48194046..48194997,4	K562	blood:
6	chr7:47984558..47985573-chr7:48194072..48195154,6	MCF-7	breast:
7	chr7:47984841..47985353-chr7:48149509..48150107,2	MCF-7	breast:
8	chr7:47984273..47985665-chr7:48007663..48009312,11	MCF-7	breast:
9	chr7:47984581..47985500-chr7:48008161..48008952,2	K562	blood:
10	chr7:47931791..47933377-chr7:47983973..47986436,2	K562	blood:
11	chr7:47984580..47985444-chr7:48147461..48148213,2	MCF-7	breast:
12	chr7:47984460..47985513-chr7:48149453..48150415,8	K562	blood:

No data

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125242	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11766127	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702399	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702400	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13229586	0.92[EUR][1000 genomes]
rs13239959	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13240488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17711336	1.00[JPT][hapmap]
rs17711348	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280537	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs3176483	0.89[EUR][1000 genomes]
rs3176493	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs3176559	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs3176565	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs35796271	0.92[EUR][1000 genomes]
rs6463456	0.95[EUR][1000 genomes]
rs6956732	0.88[JPT][hapmap]
rs71547873	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13239855	UPP1	cis	cerebellum	SCAN
rs13239855	NACAD	cis	parietal	SCAN
rs13239855	SNORA9	cis	cerebellum	SCAN
rs13239855	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
3	chr7:47976000-47986000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
7	chr7:47978600-47992600	Weak transcription	Primary B cells from cord blood	blood
8	chr7:47979600-47986000	Enhancers	HUVEC	blood vessel
9	chr7:47980600-47986200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:47980800-47989800	Weak transcription	Fetal Lung	lung
12	chr7:47980800-47993000	Weak transcription	Fetal Stomach	stomach
13	chr7:47981000-47986000	Weak transcription	Fetal Intestine Small	intestine
14	chr7:47981000-47986200	Weak transcription	Fetal Intestine Large	intestine
15	chr7:47981200-47985600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:47981200-47991400	Weak transcription	Colonic Mucosa	Colon
17	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
18	chr7:47981400-47986000	Weak transcription	NHEK	skin
19	chr7:47981400-47986200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:47981400-47989400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:47981800-47986000	Weak transcription	Right Ventricle	heart
22	chr7:47981800-47986000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:47981800-47986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:47981800-47989800	Weak transcription	Brain Substantia Nigra	brain
25	chr7:47981800-47989800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr7:47981800-47990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:47981800-47990800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:47981800-47991200	Weak transcription	A549	lung
29	chr7:47981800-47991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:47982000-47986000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:47982000-47986000	Weak transcription	HMEC	breast
32	chr7:47982000-47989800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:47982000-47990000	Weak transcription	NH-A	brain
34	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:47982400-47989400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:47982400-47992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:47982800-47985400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:47983400-47987600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:47983600-47985400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:47983600-47986000	Weak transcription	Lung	lung
44	chr7:47983600-47987000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:47983600-47987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:47983600-47987600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:47983600-47989800	Weak transcription	Right Atrium	heart
48	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:47983600-47993800	Weak transcription	Osteobl	bone
50	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--

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