Variant report

Variant	rs6560316
Chromosome Location	chr9:71323008-71323009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71318506..71320929-chr9:71321155..71324459,4	K562	blood:
2	chr9:71317469..71321528-chr9:71322199..71324795,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM122A-1	chr9:71322519-71323057	NONHSAT131754

Variant related genes	Relation type
ENSG00000107242	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10121993	0.90[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10217316	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10746919	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10781117	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10781119	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869225	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869245	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11143568	0.82[EUR][1000 genomes]
rs2151416	0.83[ASN][1000 genomes]
rs2151417	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2151418	0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2184117	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4352908	0.80[ASN][1000 genomes]
rs4534183	0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744680	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744683	0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs4744685	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4745223	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs4745227	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4745229	0.80[ASN][1000 genomes]
rs4745230	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7021661	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7853748	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs7857057	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS 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
4	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv2757339	chr9:71291107-71353743	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2759693	chr9:71291107-71353743	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2752385	chr9:71304465-71332240	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71319200-71323400	Active TSS	Rectal Smooth Muscle	rectum
2	chr9:71319600-71323200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:71320800-71324200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr9:71321200-71323200	Active TSS	Fetal Intestine Small	intestine
5	chr9:71321600-71323600	Flanking Active TSS	GM12878-XiMat	blood
6	chr9:71321800-71329200	Weak transcription	Gastric	stomach
7	chr9:71321800-71329400	Weak transcription	Lung	lung
8	chr9:71322000-71323400	Active TSS	Colonic Mucosa	Colon
9	chr9:71322000-71324800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:71322000-71329800	Weak transcription	Pancreas	Pancrea
11	chr9:71322000-71349400	Weak transcription	Aorta	Aorta
12	chr9:71322200-71323600	Enhancers	Small Intestine	intestine
13	chr9:71322200-71324400	Enhancers	Primary B cells from peripheral blood	blood
14	chr9:71322200-71324800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:71322200-71329400	Weak transcription	Left Ventricle	heart
16	chr9:71322200-71335000	Weak transcription	Placenta	Placenta
17	chr9:71322400-71323400	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr9:71322400-71325000	Enhancers	Fetal Heart	heart
19	chr9:71322400-71325800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:71322600-71323400	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:71322600-71323400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:71322600-71324800	Weak transcription	Brain Germinal Matrix	brain
23	chr9:71322600-71327400	Enhancers	HepG2	liver
24	chr9:71322600-71329600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:71322600-71329800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:71322800-71323200	Active TSS	Fetal Intestine Large	intestine
27	chr9:71322800-71323200	Weak transcription	K562	blood
28	chr9:71322800-71323600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:71322800-71323800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr9:71322800-71324200	Weak transcription	Right Atrium	heart
31	chr9:71322800-71325200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr9:71322800-71326200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:71322800-71326800	Weak transcription	Right Ventricle	heart
34	chr9:71322800-71333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:71323000-71324200	Weak transcription	Stomach Mucosa	stomach
36	chr9:71323000-71326200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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