Variant report

Variant	rs3802394
Chromosome Location	chr9:21864535-21864536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:21864530-21864881	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000265194	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10117507	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811635	0.86[GIH][hapmap];0.91[TSI][hapmap]
rs10965165	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10965168	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10965174	0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10965175	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11526324	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11531660	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11536713	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12236681	0.81[AMR][1000 genomes]
rs12236836	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12238536	0.82[AMR][1000 genomes]
rs12553901	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4352938	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4587423	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4636295	0.80[GIH][hapmap];0.84[MEX][hapmap]
rs4977569	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4977734	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs4977735	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4977736	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4977742	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4977743	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4977744	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4977745	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62556506	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62556519	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62556520	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7044807	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756641	0.95[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7850937	0.84[MEX][hapmap]
rs7851133	0.84[MEX][hapmap]
rs7865071	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802394	MTAP	cis	multi-tissue	Pritchard
rs3802394	MTAP	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21841800-21864600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:21846600-21869800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:21847600-21871600	Strong transcription	Dnd41	blood
4	chr9:21848000-21869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:21848800-21866000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:21849000-21865800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:21849000-21868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr9:21849000-21870000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:21849000-21870200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:21849200-21866200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:21849600-21864600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:21851400-21866800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:21852600-21866000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:21853600-21864600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:21853800-21866800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:21854200-21865800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:21854200-21866000	Strong transcription	Adipose Nuclei	Adipose
18	chr9:21854200-21870200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr9:21854400-21866000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:21854400-21866200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:21854400-21869800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:21854600-21864600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:21854600-21866400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:21854600-21867000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:21854800-21866400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:21855400-21873000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
28	chr9:21855800-21868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:21855800-21870600	Strong transcription	HMEC	breast
30	chr9:21856600-21871200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:21856800-21864600	Weak transcription	Gastric	stomach
32	chr9:21857000-21871200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:21857200-21866200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
35	chr9:21858200-21866200	Strong transcription	HSMM	muscle
36	chr9:21859000-21864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr9:21860000-21865400	Weak transcription	Colon Smooth Muscle	Colon
39	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
40	chr9:21860400-21864600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:21860400-21864600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:21860400-21864600	Weak transcription	Aorta	Aorta
43	chr9:21860400-21864600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:21860400-21864600	Weak transcription	Fetal Intestine Large	intestine
45	chr9:21860400-21864600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:21860400-21867200	Weak transcription	Brain Angular Gyrus	brain
47	chr9:21860400-21867200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:21860400-21868600	Weak transcription	Thymus	Thymus
49	chr9:21861400-21865800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:21861800-21864600	Weak transcription	NHLF	lung

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