Variant report

Variant	rs6601564
Chromosome Location	chr8:10982051-10982052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTMR9-1	chr8:10980891-10982326	ENSG00000247665
2	lnc-AF131215.3.1-1	chr8:10980891-10982327	ENSG00000254936.3
3	lnc-AF131215.3.1-1	chr8:10980891-10982327	ENSG00000254936.3
4	lnc-AF131215.3.1-1	chr8:10980891-10982327	NONHSAT125036

Extended variants
information (count: 81 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10087081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10089518	0.90[MEX][hapmap]
rs10105315	0.81[CEU][hapmap]
rs10105377	1.00[ASN][1000 genomes]
rs10106207	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10106914	1.00[CHB][hapmap]
rs10108618	0.90[MEX][hapmap]
rs10113808	0.81[CEU][hapmap]
rs10503415	1.00[JPT][hapmap]
rs10503416	1.00[CHB][hapmap]
rs1057626	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11250117	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11250119	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11773990	0.85[CEU][hapmap]
rs11991118	0.81[CEU][hapmap];0.95[MEX][hapmap]
rs12546366	0.80[MEX][hapmap]
rs17724467	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17783634	1.00[CHB][hapmap]
rs2001329	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001433	0.88[CEU][hapmap]
rs2409689	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs2409691	0.95[MEX][hapmap]
rs2409710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409712	1.00[CHB][hapmap]
rs2409713	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2409714	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2409715	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2409716	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2409717	0.92[ASN][1000 genomes]
rs2409718	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2409742	1.00[CHB][hapmap]
rs28417109	1.00[ASN][1000 genomes]
rs28630509	0.89[ASN][1000 genomes]
rs2898257	0.89[CEU][hapmap]
rs2898260	0.85[CEU][hapmap]
rs3021494	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap]
rs3021500	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34208825	0.82[EUR][1000 genomes]
rs34772085	1.00[ASN][1000 genomes]
rs4333549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4523214	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4840544	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4840549	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4840551	0.84[EUR][1000 genomes]
rs4841489	0.85[CEU][hapmap]
rs4841490	0.88[CEU][hapmap]
rs4841495	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4841498	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4841500	1.00[CHB][hapmap]
rs4841501	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4841503	0.82[EUR][1000 genomes]
rs4841504	0.81[CEU][hapmap];0.87[GIH][hapmap];0.80[EUR][1000 genomes]
rs4841507	0.82[CHB][hapmap]
rs60921132	0.97[ASN][1000 genomes]
rs6601560	0.82[CEU][hapmap]
rs6601562	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6980856	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs6986032	1.00[CHB][hapmap]
rs6991930	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6995204	0.94[ASN][1000 genomes]
rs6996752	0.88[CHD][hapmap]
rs6996846	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004825	0.82[JPT][hapmap]
rs7005680	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7010590	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap]
rs7011756	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7460507	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs7813802	1.00[CHB][hapmap]
rs7819412	0.82[CHB][hapmap]
rs7820860	0.80[CEU][hapmap]
rs7823349	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs7829396	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9657519	0.81[CEU][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1027845	chr8:10959666-10995565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv1019796	chr8:10979442-11010826	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6601564	PRSS55	cis	cerebellum	SCAN
rs6601564	TDH	cis	cerebellum	SCAN
rs6601564	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs6601564	AF131215.9	cis	Esophagus Mucosa	GTEx
rs6601564	CTSB	cis	cerebellum	SCAN
rs6601564	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs6601564	MFHAS1	cis	cerebellum	SCAN
rs6601564	DEFB134	cis	cerebellum	SCAN
rs6601564	AF131215.9	cis	Nerve Tibial	GTEx
rs6601564	AF131215.2	cis	Stomach	GTEx
rs6601564	C8orf5	cis	normal skin	skin_eQTL
rs6601564	AF131215.2	cis	Nerve Tibial	GTEx
rs6601564	FLJ10661	cis	cerebellum	SCAN
rs6601564	TDH	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:10981200-10982200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr8:10981200-10982400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr8:10981200-10982800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:10981400-10982200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:10981400-10982200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr8:10981400-10982400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr8:10981400-10982400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:10981400-10982400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr8:10981400-10982400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:10981400-10982400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr8:10981400-10982400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr8:10981400-10982400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:10981400-10982400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:10981400-10982800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr8:10981400-10983000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr8:10981400-10983000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr8:10981400-10983000	Enhancers	Lung	lung
20	chr8:10981400-10983200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr8:10981400-10983200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:10981600-10982200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr8:10981600-10982200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr8:10981600-10982200	Active TSS	Primary B cells from peripheral blood	blood
25	chr8:10981600-10982200	Active TSS	Primary T cells fromperipheralblood	blood
26	chr8:10981600-10982200	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr8:10981600-10982200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:10981600-10982200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr8:10981600-10982400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr8:10981600-10982400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr8:10981600-10982600	Weak transcription	Spleen	Spleen
32	chr8:10981600-10982600	Active TSS	GM12878-XiMat	blood
33	chr8:10981600-10982800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:10981600-10983000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr8:10981600-10983000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr8:10981800-10982400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr8:10981800-10982400	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr8:10981800-10982400	Active TSS	Monocytes-CD14+_RO01746	blood
39	chr8:10981800-10983200	Enhancers	Primary T cells from cord blood	blood
40	chr8:10982000-10982200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr8:10982000-10982200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr8:10982000-10982400	Active TSS	Primary B cells from cord blood	blood
43	chr8:10982000-10982400	Active TSS	Primary hematopoietic stem cells	blood
44	chr8:10982000-10982800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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