Variant report

Variant	rs12649852
Chromosome Location	chr4:15982480-15982481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10013583	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12498478	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12512355	0.85[CEU][hapmap]
rs17477869	0.95[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2240682	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240685	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs3796855	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3815344	0.89[AMR][1000 genomes];0.97[EUR][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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12649852	UTS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15940200-15983600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:15965200-15983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:15965600-15984000	Weak transcription	Colonic Mucosa	Colon
5	chr4:15967800-15983600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:15968000-16002600	Weak transcription	Left Ventricle	heart
7	chr4:15968600-15993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:15968800-15983600	Weak transcription	Pancreas	Pancrea
9	chr4:15968800-15992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:15969600-15990000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
12	chr4:15969800-15986200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:15971000-15983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:15971000-15992200	Weak transcription	Fetal Brain Male	brain
15	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
16	chr4:15973200-15993800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:15974000-15991800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:15976400-15985800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:15976600-15984400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:15976800-16002600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:15977000-16007400	Weak transcription	Gastric	stomach
22	chr4:15978000-15996800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:15978200-16003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:15978600-15984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:15978800-15983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:15978800-15984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:15978800-16002800	Weak transcription	Right Ventricle	heart
28	chr4:15979400-16000400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:15979600-15996600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr4:15979600-15998800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:15980400-15983200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:15980400-15983400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:15980400-15983600	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:15980600-15982600	Weak transcription	Fetal Stomach	stomach
35	chr4:15980600-15983200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:15980800-15983200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:15981000-15983600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:15981200-15983600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:15981800-15983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:15981800-15983400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:15982000-15983200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:15982000-15983400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:15982000-15988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:15982200-15983000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:15982200-16008200	Weak transcription	Brain Germinal Matrix	brain
46	chr4:15982400-15982800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:15982400-15988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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