Variant report

Variant	rs5999095
Chromosome Location	chr22:34172049-34172050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34167046..34169223-chr22:34170241..34173338,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11089631	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11703278	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11705248	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12167740	0.95[ASN][1000 genomes]
rs12169879	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12170014	0.93[ASN][1000 genomes]
rs12484459	0.88[ASN][1000 genomes]
rs12628434	0.97[ASN][1000 genomes]
rs13053313	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2267282	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267285	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267293	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267294	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2283939	0.83[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs2283943	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283944	0.82[ASN][1000 genomes]
rs2283945	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2283946	0.87[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2283949	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4820111	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820112	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820113	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4821182	0.89[GIH][hapmap]
rs619426	0.83[ASN][1000 genomes]
rs715482	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73170589	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs743704	0.82[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs743705	0.87[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8138783	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9619374	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1055203	chr22:34098417-34196685	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv459878	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv588936	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv529885	chr22:34150132-34182300	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1064781	chr22:34152145-34231792	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv529886	chr22:34153740-34258847	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv2758542	chr22:34169795-34203479	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2758833	chr22:34169795-34203479	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3369939	chr22:34172007-34172449	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5999095	RNF215	cis	parietal	SCAN
rs5999095	HSCB	cis	parietal	SCAN
rs5999095	PLA2G3	cis	parietal	SCAN
rs5999095	LIMK2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
2	chr22:34154400-34175800	Weak transcription	Fetal Stomach	stomach
3	chr22:34154400-34176000	Weak transcription	Gastric	stomach
4	chr22:34162600-34172600	Weak transcription	Lung	lung
5	chr22:34165400-34176400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr22:34165600-34172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:34166000-34172200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:34166000-34176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr22:34166800-34175800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr22:34167600-34172200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr22:34167800-34176000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr22:34168000-34173000	Weak transcription	Pancreas	Pancrea
13	chr22:34168000-34183800	Enhancers	Fetal Heart	heart
14	chr22:34169000-34176000	Weak transcription	Fetal Muscle Leg	muscle
15	chr22:34169200-34172400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:34169400-34177600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:34169800-34176200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr22:34170000-34181800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr22:34170800-34172800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr22:34170800-34173000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr22:34170800-34174000	Enhancers	Psoas Muscle	Psoas
22	chr22:34170800-34174600	Enhancers	Left Ventricle	heart
23	chr22:34171000-34172800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr22:34171000-34174600	Enhancers	Ovary	ovary
25	chr22:34171400-34172600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr22:34171400-34172600	Weak transcription	Fetal Lung	lung
27	chr22:34171400-34172600	Weak transcription	Right Ventricle	heart
28	chr22:34171400-34172800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:34171400-34172800	Weak transcription	Right Atrium	heart
30	chr22:34171400-34172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr22:34171400-34176000	Weak transcription	Colon Smooth Muscle	Colon
32	chr22:34171600-34172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr22:34171600-34174400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr22:34171600-34176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr22:34171800-34174600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr22:34172000-34172200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:34172000-34172200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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