Variant report

Variant	rs2975868
Chromosome Location	chr9:72705607-72705608
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-1	chr9:72705522-72705706	ENSG00000204706.10
2	lnc-KLF9-1	chr9:72705522-72705710	NONHSAT131795

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10114215	0.83[ASN][1000 genomes]
rs10511979	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1073540	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1112232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180101	0.92[CHB][hapmap]
rs1180102	0.92[CHB][hapmap]
rs1180104	0.92[CHB][hapmap]
rs1180105	0.92[CHB][hapmap]
rs1180107	0.92[CHB][hapmap]
rs1180112	0.91[CHB][hapmap]
rs1180117	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1180118	0.92[CHB][hapmap]
rs1180122	0.92[CHB][hapmap]
rs1180124	0.91[CHB][hapmap]
rs1180126	0.92[CHB][hapmap]
rs12002407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12003971	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683706	0.85[ASN][1000 genomes]
rs12683986	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12684987	0.85[ASN][1000 genomes]
rs12685632	0.90[ASN][1000 genomes]
rs12685937	0.88[ASN][1000 genomes]
rs12685939	0.90[ASN][1000 genomes]
rs12686383	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686573	0.81[ASN][1000 genomes]
rs12686668	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12686850	0.83[ASN][1000 genomes]
rs17052443	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs17087686	0.91[ASN][1000 genomes]
rs17088796	0.85[ASN][1000 genomes]
rs17088840	0.85[ASN][1000 genomes]
rs17088889	0.85[ASN][1000 genomes]
rs17088905	0.83[ASN][1000 genomes]
rs17523363	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927105	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927110	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927116	0.85[ASN][1000 genomes]
rs1927117	0.83[ASN][1000 genomes]
rs1927119	0.83[ASN][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs1927150	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1986412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001235	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2148865	0.83[ASN][1000 genomes]
rs2296772	0.93[ASN][1000 genomes]
rs2296773	0.93[ASN][1000 genomes]
rs2309584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2871290	0.85[ASN][1000 genomes]
rs2975866	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975867	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975880	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2975884	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2975911	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2997668	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2997679	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2997681	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2997714	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3015165	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015169	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015170	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015171	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3015173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015174	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015175	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015177	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015180	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015184	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015198	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015204	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015207	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015213	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015223	0.96[ASN][1000 genomes]
rs35188046	0.85[ASN][1000 genomes]
rs3829096	0.89[ASN][1000 genomes]
rs4289878	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460447	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4495496	0.93[ASN][1000 genomes]
rs4744982	0.85[ASN][1000 genomes]
rs4744994	0.92[CHB][hapmap]
rs56735283	0.81[ASN][1000 genomes]
rs57048128	0.81[ASN][1000 genomes]
rs58085049	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58660710	0.90[ASN][1000 genomes]
rs58969772	0.83[ASN][1000 genomes]
rs59189596	0.85[ASN][1000 genomes]
rs59589460	0.85[ASN][1000 genomes]
rs59619263	0.85[ASN][1000 genomes]
rs61265226	0.83[ASN][1000 genomes]
rs61416419	0.93[ASN][1000 genomes]
rs7022893	0.83[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs716535	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs72709197	0.90[ASN][1000 genomes]
rs72709200	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72710469	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72710483	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745852	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867595	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943536	0.92[CHB][hapmap]
rs943540	0.92[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv949052	chr9:72698039-72741247	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2975868	MAMDC2	cis	parietal	SCAN
rs2975868	C9orf71	cis	cerebellum	SCAN
rs2975868	C9orf85	cis	parietal	SCAN
rs2975868	ALDH1A1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72694800-72708200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr9:72694800-72721400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:72695400-72709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:72696400-72706200	Weak transcription	Left Ventricle	heart
5	chr9:72696400-72706600	Weak transcription	Fetal Brain Female	brain
6	chr9:72696400-72708800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:72696800-72705800	Weak transcription	HSMM	muscle
8	chr9:72698200-72706000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:72698200-72708800	Weak transcription	Psoas Muscle	Psoas
10	chr9:72698800-72711200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:72699000-72708800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:72701600-72706400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:72701600-72706600	Weak transcription	Adipose Nuclei	Adipose
14	chr9:72702000-72707200	Weak transcription	Pancreas	Pancrea
15	chr9:72702200-72706000	Weak transcription	Ovary	ovary
16	chr9:72702200-72706200	Weak transcription	Right Ventricle	heart
17	chr9:72703200-72711600	Enhancers	Colon Smooth Muscle	Colon
18	chr9:72703600-72705800	Weak transcription	HSMMtube	muscle
19	chr9:72703600-72706400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:72704600-72706200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:72704800-72708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:72705400-72706200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:72705400-72709400	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:72705600-72706600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr9:72705600-72706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:72705600-72707800	Enhancers	Stomach Smooth Muscle	stomach

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