Variant report

Variant	rs7860486
Chromosome Location	chr9:71157459-71157460
allele	A/C
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	chr9:71157392-71157476	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGM5-1	chr9:71157294-71157558	ENSG00000226337.2
2	lnc-PGM5-1	chr9:71157294-71157558	NONHSAT131748
3	lnc-PGM5-1	chr9:71157294-71157558	ENSG00000226337.3

Variant related genes	Relation type
TMEM252	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10120859	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10735603	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869001	0.95[GIH][hapmap]
rs10869020	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10869034	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10869043	0.89[ASN][1000 genomes]
rs11795256	0.89[ASN][1000 genomes]
rs12340143	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12343877	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12376362	0.86[ASN][1000 genomes]
rs13285683	0.82[ASN][1000 genomes]
rs1411992	0.87[ASN][1000 genomes]
rs265073	0.81[GIH][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs3920702	0.83[ASN][1000 genomes]
rs398222	0.88[ASN][1000 genomes]
rs404994	0.81[YRI][hapmap]
rs4143073	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4457398	0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4745093	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6560203	0.88[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7028200	0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs7036795	0.89[ASN][1000 genomes]
rs7046767	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7861495	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893413	chr9:71130848-71196984	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893411	chr9:71130848-71199545	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv893412	chr9:71130848-71199545	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1024967	chr9:71130848-71210031	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv482506	chr9:71130848-71280888	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv466392	chr9:71130848-71318817	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv614546	chr9:71130848-71318817	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv893414	chr9:71139378-71320732	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71139600-71161600	Weak transcription	Spleen	Spleen
2	chr9:71145800-71161600	Weak transcription	Gastric	stomach
3	chr9:71152200-71161600	Weak transcription	Right Ventricle	heart
4	chr9:71152200-71170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:71153800-71161800	Weak transcription	Psoas Muscle	Psoas
6	chr9:71154200-71161600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:71155600-71161400	Weak transcription	Lung	lung
8	chr9:71155800-71157600	Enhancers	Fetal Intestine Large	intestine
9	chr9:71155800-71161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:71156200-71157600	Enhancers	Fetal Intestine Small	intestine
11	chr9:71156600-71161400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:71156600-71161600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:71156600-71161600	Weak transcription	HepG2	liver
14	chr9:71156800-71157800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:71156800-71161400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:71157000-71157600	Enhancers	Left Ventricle	heart
17	chr9:71157000-71160000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:71157000-71160000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr9:71157000-71161400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:71157000-71161400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:71157200-71157600	Enhancers	Fetal Kidney	kidney
22	chr9:71157200-71161400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:71157200-71161400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:71157200-71165600	Weak transcription	Stomach Mucosa	stomach
25	chr9:71157200-71166000	Weak transcription	Colonic Mucosa	Colon
26	chr9:71157400-71160200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:71157400-71160600	Weak transcription	Right Atrium	heart
28	chr9:71157400-71161400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:71157400-71161400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:71157400-71161400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:71157400-71166000	Weak transcription	Fetal Heart	heart

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