Variant report

Variant	rs867595
Chromosome Location	chr9:72694541-72694542
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10114215	0.80[ASN][1000 genomes]
rs10511979	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1073540	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1112232	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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]
rs12002407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12003971	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12683706	0.82[ASN][1000 genomes]
rs12683986	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12684987	0.82[ASN][1000 genomes]
rs12685632	0.93[ASN][1000 genomes]
rs12685937	0.91[ASN][1000 genomes]
rs12685939	0.93[ASN][1000 genomes]
rs12686383	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12686668	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17052443	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs17087686	0.95[ASN][1000 genomes]
rs17088796	0.82[ASN][1000 genomes]
rs17088840	0.82[ASN][1000 genomes]
rs17088889	0.82[ASN][1000 genomes]
rs17523363	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927105	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927110	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927116	0.82[ASN][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs1927150	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1986412	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001235	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296772	0.90[ASN][1000 genomes]
rs2296773	0.90[ASN][1000 genomes]
rs2309584	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2871290	0.82[ASN][1000 genomes]
rs2975866	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2975867	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2975868	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2975880	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2975884	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2975911	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2997668	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2997679	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997681	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2997714	0.96[ASN][1000 genomes]
rs3015165	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015169	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015170	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015171	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015173	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015174	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015175	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015177	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015181	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015182	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015184	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015185	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015186	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015189	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015198	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015204	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015207	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015213	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015223	0.92[ASN][1000 genomes]
rs35188046	0.82[ASN][1000 genomes]
rs3829096	0.93[ASN][1000 genomes]
rs4289878	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4460447	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4495496	0.90[ASN][1000 genomes]
rs4744982	0.82[ASN][1000 genomes]
rs4744994	0.92[CHB][hapmap]
rs58085049	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58660710	0.93[ASN][1000 genomes]
rs58969772	0.80[ASN][1000 genomes]
rs59189596	0.82[ASN][1000 genomes]
rs59589460	0.82[ASN][1000 genomes]
rs59619263	0.82[ASN][1000 genomes]
rs61416419	0.96[ASN][1000 genomes]
rs7022893	0.80[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs716535	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs72709197	0.93[ASN][1000 genomes]
rs72709200	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72710469	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710483	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs745852	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs943540	0.92[CHB][hapmap];0.91[JPT][hapmap]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs867595	C9orf85	cis	parietal	SCAN
rs867595	MAMDC2	cis	parietal	SCAN
rs867595	ALDH1A1	cis	cerebellum	SCAN
rs867595	C9orf71	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72685000-72694600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:72685200-72695800	Weak transcription	Aorta	Aorta
3	chr9:72685200-72696000	Weak transcription	Right Atrium	heart
4	chr9:72687200-72694800	Strong transcription	HSMMtube	muscle
5	chr9:72688600-72695200	Weak transcription	HSMM	muscle
6	chr9:72688600-72696400	Enhancers	Ovary	ovary
7	chr9:72689000-72695600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:72689200-72694600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:72689400-72696200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:72690200-72695200	Enhancers	Colon Smooth Muscle	Colon
11	chr9:72690600-72695600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:72690600-72696200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:72693400-72696600	Enhancers	Fetal Stomach	stomach
14	chr9:72693800-72694600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr9:72693800-72694600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:72693800-72694800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:72693800-72694800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:72693800-72694800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr9:72693800-72695000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr9:72693800-72695000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:72693800-72695000	Enhancers	Pancreas	Pancrea
22	chr9:72693800-72695800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:72693800-72696400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:72693800-72696400	Enhancers	Fetal Muscle Leg	muscle
25	chr9:72693800-72696800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr9:72694000-72694600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr9:72694000-72694600	Enhancers	Fetal Lung	lung
28	chr9:72694000-72694800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr9:72694000-72694800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr9:72694000-72694800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr9:72694000-72694800	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr9:72694000-72695000	Enhancers	Psoas Muscle	Psoas
33	chr9:72694000-72695200	Enhancers	Brain Germinal Matrix	brain
34	chr9:72694000-72696000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:72694000-72696000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr9:72694000-72696200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr9:72694000-72696200	Enhancers	Lung	lung
38	chr9:72694000-72696400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:72694000-72696400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:72694000-72696800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr9:72694000-72696800	Enhancers	Adipose Nuclei	Adipose
42	chr9:72694200-72694600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr9:72694200-72695200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:72694200-72695800	Enhancers	Fetal Brain Male	brain
45	chr9:72694200-72696600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:72694200-72697000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:72694400-72694600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr9:72694400-72696000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:72694400-72696400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:72694400-72696400	Enhancers	NHLF	lung

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