Variant report

Variant	rs7869004
Chromosome Location	chr9:21931896-21931897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf53-5	chr9:21930389-21932738	NONHSAT130406

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10811638	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs10965183	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965186	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2188125	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518712	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2518713	0.89[CEU][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2518714	0.89[CEU][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2518715	0.89[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2811715	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4977570	1.00[CEU][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4977746	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4977747	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4977748	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977749	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6475597	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852128	0.80[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7852234	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864029	0.94[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7869004	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21911000-21935800	Weak transcription	HSMM	muscle
2	chr9:21919800-21932800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:21920600-21935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:21920600-21942600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:21920800-21932000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:21921200-21934000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:21921200-21935600	Weak transcription	Primary T cells from cord blood	blood
8	chr9:21922200-21932400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:21922200-21933000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:21923800-21934000	Weak transcription	Thymus	Thymus
11	chr9:21923800-21934800	Weak transcription	Dnd41	blood
12	chr9:21924000-21934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:21924800-21933000	Weak transcription	Lung	lung
14	chr9:21927000-21933400	Weak transcription	HSMMtube	muscle
15	chr9:21928000-21934800	Weak transcription	Psoas Muscle	Psoas
16	chr9:21928600-21933200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:21928800-21933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:21929200-21932600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:21929600-21932800	Weak transcription	Gastric	stomach
20	chr9:21929600-21933800	Weak transcription	Liver	Liver
21	chr9:21929800-21935600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:21930000-21932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:21930000-21932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:21930000-21932600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:21930000-21932600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:21930200-21932200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:21930200-21932600	Weak transcription	Spleen	Spleen
28	chr9:21930400-21932600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:21930800-21932000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:21930800-21932000	Strong transcription	Ovary	ovary
31	chr9:21930800-21933800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:21931000-21932000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:21931000-21932000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr9:21931000-21932000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:21931000-21932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:21931000-21932000	Strong transcription	Aorta	Aorta
37	chr9:21931000-21932000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr9:21931000-21932000	Strong transcription	Fetal Stomach	stomach
39	chr9:21931000-21932000	Strong transcription	Left Ventricle	heart
40	chr9:21931000-21932400	Strong transcription	Adipose Nuclei	Adipose
41	chr9:21931000-21933400	Weak transcription	Placenta	Placenta
42	chr9:21931200-21932000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:21931400-21932000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:21931400-21934600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:21931400-21937400	Weak transcription	Pancreas	Pancrea
46	chr9:21931600-21933400	Weak transcription	Right Ventricle	heart
47	chr9:21931600-21933400	Weak transcription	NHDF-Ad	bronchial
48	chr9:21931600-21935600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:21931800-21932000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:21931800-21932000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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