Variant report

Variant	rs17012080
Chromosome Location	chr4:87719696-87719697
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17012069	0.81[AFR][1000 genomes]
rs17012084	1.00[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012088	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73838343	0.86[AFR][1000 genomes];1.00[AMR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17012080	RAGE	trans	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
2	chr4:87639400-87739200	Weak transcription	A549	lung
3	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
6	chr4:87689400-87738200	Weak transcription	Gastric	stomach
7	chr4:87690000-87738800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:87690800-87736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:87692800-87734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:87694400-87724800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:87694400-87725200	Weak transcription	NH-A	brain
12	chr4:87694400-87735600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:87695600-87728600	Weak transcription	Adipose Nuclei	Adipose
14	chr4:87696800-87733600	Weak transcription	NHLF	lung
15	chr4:87698200-87728600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:87698600-87738600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:87712000-87736600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:87712400-87728800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:87712600-87720400	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:87712600-87721000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:87712600-87721800	Weak transcription	Esophagus	oesophagus
22	chr4:87712600-87724600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:87712600-87728600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:87712600-87733600	Weak transcription	Lung	lung
25	chr4:87712600-87735800	Weak transcription	Brain Germinal Matrix	brain
26	chr4:87712600-87737600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:87712600-87738400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:87712600-87751400	Weak transcription	Aorta	Aorta
29	chr4:87712800-87720200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:87712800-87720400	Weak transcription	Fetal Stomach	stomach
31	chr4:87712800-87721200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:87712800-87732000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:87712800-87736400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:87712800-87737000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:87712800-87739600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:87713200-87720400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:87713200-87728600	Weak transcription	Ovary	ovary
38	chr4:87713400-87721800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:87714000-87722600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:87714400-87720200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:87714400-87731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:87714600-87720800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:87715600-87732600	Weak transcription	Brain Substantia Nigra	brain
44	chr4:87715800-87737400	Weak transcription	Colon Smooth Muscle	Colon
45	chr4:87717200-87737000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:87717600-87730800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:87717600-87731000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:87717800-87732400	Weak transcription	Fetal Thymus	thymus
49	chr4:87718000-87732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:87719000-87721800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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