Variant report

Variant	rs6897517
Chromosome Location	chr5:115705696-115705697
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115704428..115706706-chr5:115709540..115711421,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA6A-1	chr5:115703287-115706170	ENSG00000249280
2	lnc-SEMA6A-1	chr5:115703113-115706170	NONHSAT103361

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10037895	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10054441	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056823	0.81[TSI][hapmap]
rs10063312	0.82[CHD][hapmap];0.83[TSI][hapmap]
rs11241374	0.84[CHD][hapmap];0.83[TSI][hapmap]
rs12109104	0.82[CHD][hapmap];0.81[TSI][hapmap]
rs12516272	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12657249	0.81[CHD][hapmap];0.81[TSI][hapmap]
rs1421846	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421847	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1677415	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs185263	0.90[JPT][hapmap]
rs253950	0.82[CHD][hapmap]
rs253959	0.82[CHD][hapmap]
rs253961	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs254151	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs254174	0.83[CHD][hapmap];0.80[TSI][hapmap]
rs27368	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28031	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594966	0.81[AMR][1000 genomes]
rs6594967	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7701723	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7705679	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708765	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7719798	0.81[AMR][1000 genomes]
rs929752	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9327000	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2763489	chr5:115693166-115733327	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6897517	COMMD10	cis	lymphoblastoid	seeQTL
rs6897517	COMMD10	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115684400-115705800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr5:115685000-115721400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:115687200-115706400	Weak transcription	Liver	Liver
4	chr5:115694400-115707800	Weak transcription	Spleen	Spleen
5	chr5:115695800-115706600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:115695800-115714600	Weak transcription	Thymus	Thymus
7	chr5:115696000-115708000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:115696400-115707600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:115696400-115708400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:115697600-115707400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:115697600-115708200	Weak transcription	Lung	lung
12	chr5:115697600-115712000	Weak transcription	Aorta	Aorta
13	chr5:115697600-115714000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:115697600-115748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:115697800-115706600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:115697800-115706800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:115697800-115708200	Weak transcription	Psoas Muscle	Psoas
18	chr5:115697800-115708400	Weak transcription	Colonic Mucosa	Colon
19	chr5:115698000-115722800	Weak transcription	Pancreas	Pancrea
20	chr5:115698400-115714000	Weak transcription	Right Ventricle	heart
21	chr5:115699400-115710200	Weak transcription	Primary B cells from cord blood	blood
22	chr5:115701400-115706200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:115702800-115706000	Weak transcription	Fetal Kidney	kidney
24	chr5:115705200-115706800	Enhancers	K562	blood
25	chr5:115705200-115707400	Enhancers	Primary T cells from cord blood	blood
26	chr5:115705200-115713000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:115705400-115705800	Enhancers	Left Ventricle	heart
28	chr5:115705400-115706000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr5:115705400-115706200	Enhancers	Fetal Thymus	thymus
30	chr5:115705400-115706600	Enhancers	HUVEC	blood vessel
31	chr5:115705400-115706800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr5:115705400-115707200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr5:115705600-115706000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:115705600-115706000	Enhancers	Right Atrium	heart
35	chr5:115705600-115706200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:115705600-115706800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:115705600-115707200	Weak transcription	Adipose Nuclei	Adipose
38	chr5:115705600-115707400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:115705600-115708200	Weak transcription	Esophagus	oesophagus

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