Variant report

Variant	rs6477087
Chromosome Location	chr9:6472714-6472715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10115883	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10122116	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10124572	0.87[ASN][1000 genomes]
rs10125914	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10733529	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10739098	0.82[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap]
rs10739099	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10739100	0.80[ASN][1000 genomes]
rs10758784	0.88[CEU][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10758785	0.82[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap]
rs10758788	0.84[JPT][hapmap]
rs10758789	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap]
rs10758790	0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs10758792	0.80[ASN][1000 genomes]
rs10815428	0.89[JPT][hapmap]
rs10975583	0.82[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs10975585	0.81[ASN][1000 genomes]
rs10975595	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10975603	0.97[ASN][1000 genomes]
rs10975605	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1156747	0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs11790625	0.85[ASN][1000 genomes]
rs11791651	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11795355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12346455	0.94[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12347573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351293	0.87[ASN][1000 genomes]
rs13283381	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13289925	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13291472	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13292799	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13296970	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13298500	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs13301146	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13440427	0.83[ASN][1000 genomes]
rs1381035	0.83[JPT][hapmap]
rs16924328	0.84[JPT][hapmap]
rs16924562	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs16924591	0.89[ASN][1000 genomes]
rs16924624	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16924626	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16924631	0.94[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs16924634	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1870696	0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1903419	0.88[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs2169283	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs2169286	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2282158	0.88[CHB][hapmap]
rs2297443	0.88[CHB][hapmap]
rs33962342	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs3739654	0.94[ASW][hapmap];0.83[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3818705	0.94[CHB][hapmap]
rs4380997	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4384035	0.86[ASN][1000 genomes]
rs4463484	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4556138	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4740844	0.88[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4740845	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742199	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4742201	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap]
rs4742202	0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap]
rs504698	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs530722	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55960819	0.87[ASN][1000 genomes]
rs56218473	0.81[ASN][1000 genomes]
rs56396114	0.87[ASN][1000 genomes]
rs569866	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477086	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66509816	0.88[ASN][1000 genomes]
rs7027302	0.87[ASN][1000 genomes]
rs7029772	0.93[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7034328	1.00[ASN][1000 genomes]
rs73399080	0.98[ASN][1000 genomes]
rs73401025	0.86[ASN][1000 genomes]
rs7847675	0.84[ASN][1000 genomes]
rs7848831	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7852539	0.89[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857628	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7860966	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7861073	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7861559	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7865955	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7873756	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7876000	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6477087	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
2	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:6450000-6473600	Weak transcription	Small Intestine	intestine
7	chr9:6450000-6477600	Weak transcription	Left Ventricle	heart
8	chr9:6450000-6477600	Weak transcription	HSMMtube	muscle
9	chr9:6450000-6477600	Weak transcription	NHLF	lung
10	chr9:6450000-6478600	Weak transcription	Ovary	ovary
11	chr9:6450000-6482800	Weak transcription	Pancreas	Pancrea
12	chr9:6450200-6477400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:6450800-6477400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:6451000-6477600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:6451200-6475800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:6451200-6477600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:6452600-6488000	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:6452800-6476000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:6452800-6481600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:6452800-6485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:6452800-6485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:6456200-6477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:6456200-6477800	Weak transcription	Fetal Brain Female	brain
24	chr9:6458600-6476000	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:6458600-6482800	Weak transcription	Gastric	stomach
26	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
27	chr9:6459000-6477600	Weak transcription	Fetal Kidney	kidney
28	chr9:6459200-6477600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:6459200-6477800	Weak transcription	Brain Germinal Matrix	brain
30	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:6460600-6486800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:6460800-6475400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:6460800-6477600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:6461400-6486000	Weak transcription	K562	blood
35	chr9:6462600-6475800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:6462600-6477600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:6463200-6475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:6463400-6475400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
40	chr9:6463800-6476600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:6463800-6477000	Weak transcription	Lung	lung
42	chr9:6464000-6475800	Weak transcription	Adipose Nuclei	Adipose
43	chr9:6464000-6476000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:6465000-6477400	Weak transcription	NH-A	brain
45	chr9:6466600-6476600	Weak transcription	Fetal Intestine Small	intestine
46	chr9:6466800-6476600	Weak transcription	Fetal Stomach	stomach
47	chr9:6467200-6475800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:6467400-6473000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:6467400-6475200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr9:6467400-6475400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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