Variant report

Variant	rs12517400
Chromosome Location	chr5:111499041-111499042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:111008689..111010998-chr5:111497421..111499874,3	MCF-7	breast:
2	chr5:111092933..111095338-chr5:111496527..111499231,3	MCF-7	breast:
3	chr11:65657906..65658479-chr5:111498817..111499317,2	NB4	blood:
4	chr5:111100842..111103505-chr5:111497212..111499866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134986	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17134155	0.81[CEU][hapmap]
rs2416274	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7713216	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12517400	PJA2	cis	parietal	SCAN
rs12517400	AQPEP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111497200-111499200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
2	chr5:111497400-111500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:111497600-111499600	Weak transcription	Esophagus	oesophagus
4	chr5:111497600-111499800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:111497600-111500400	Weak transcription	Stomach Mucosa	stomach
6	chr5:111497600-111501400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:111497600-111502000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:111497600-111502000	Weak transcription	Aorta	Aorta
9	chr5:111497600-111538600	Weak transcription	Small Intestine	intestine
10	chr5:111497800-111499200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
11	chr5:111497800-111499400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:111497800-111499600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr5:111497800-111500000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:111497800-111504400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:111497800-111505000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr5:111497800-111505000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr5:111498000-111502600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr5:111498000-111503600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:111498000-111504800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:111498000-111504800	Strong transcription	Fetal Thymus	thymus
21	chr5:111498000-111505600	Strong transcription	Fetal Muscle Leg	muscle
22	chr5:111498000-111505600	Strong transcription	Placenta	Placenta
23	chr5:111498200-111499200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr5:111498200-111499200	Genic enhancers	Fetal Brain Female	brain
25	chr5:111498200-111499600	Weak transcription	Fetal Intestine Small	intestine
26	chr5:111498200-111499800	Genic enhancers	Fetal Heart	heart
27	chr5:111498200-111499800	Strong transcription	Rectal Smooth Muscle	rectum
28	chr5:111498200-111500200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr5:111498200-111500600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:111498200-111502200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:111498200-111502600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:111498200-111502800	Strong transcription	Ovary	ovary
33	chr5:111498200-111502800	Strong transcription	HSMM	muscle
34	chr5:111498200-111504800	Strong transcription	Fetal Intestine Large	intestine
35	chr5:111498200-111504800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:111498200-111505000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:111498200-111505600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr5:111498200-111518800	Weak transcription	Right Atrium	heart
39	chr5:111498400-111499200	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr5:111498400-111499400	Strong transcription	Fetal Brain Male	brain
41	chr5:111498400-111500200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:111498400-111500400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:111498400-111500600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:111498400-111500600	Strong transcription	Colonic Mucosa	Colon
45	chr5:111498400-111500600	Strong transcription	Gastric	stomach
46	chr5:111498400-111501000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:111498400-111501600	Strong transcription	NHDF-Ad	bronchial
48	chr5:111498400-111501800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr5:111498400-111502600	Strong transcription	HSMMtube	muscle
50	chr5:111498400-111502800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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