Variant report

Variant	rs10076661
Chromosome Location	chr5:115428755-115428756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115420483..115422692-chr5:115428367..115432405,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271918	Chromatin interaction
ENSG00000145781	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1001014	0.84[CHB][hapmap]
rs10051047	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10057200	0.87[ASN][1000 genomes]
rs10057462	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10059969	1.00[CHB][hapmap]
rs10059989	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10062588	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs10068730	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10069565	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10069947	0.86[ASN][1000 genomes]
rs10071359	1.00[CHB][hapmap]
rs10073199	1.00[CHB][hapmap]
rs10074746	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10076543	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10077113	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10477550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478286	1.00[CHB][hapmap]
rs10478287	1.00[CHB][hapmap]
rs10519444	0.84[CHB][hapmap]
rs11241379	0.84[CHB][hapmap]
rs11951682	1.00[CHB][hapmap]
rs11954350	1.00[CHB][hapmap]
rs11955144	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs11955906	1.00[CHB][hapmap]
rs11957382	1.00[CHB][hapmap]
rs11959844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12515182	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12515280	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12517505	0.90[CEU][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12522977	1.00[CHB][hapmap]
rs13356535	0.81[ASN][1000 genomes]
rs13362436	0.84[CHB][hapmap]
rs1396484	1.00[CHB][hapmap]
rs1396486	1.00[CHB][hapmap]
rs1508870	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs1508873	1.00[CHB][hapmap]
rs1543952	1.00[CHB][hapmap]
rs1567331	0.82[CHB][hapmap]
rs1567338	1.00[CHB][hapmap]
rs1567339	1.00[CHB][hapmap]
rs17138834	0.84[CHB][hapmap]
rs17138848	0.83[CHB][hapmap]
rs17138861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17138879	0.84[CHB][hapmap]
rs17139253	0.84[CHB][hapmap]
rs17139333	0.84[CHB][hapmap]
rs1876672	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1876676	1.00[CHB][hapmap]
rs2136213	0.84[CHB][hapmap]
rs2161321	1.00[CHB][hapmap]
rs2174996	1.00[CHB][hapmap]
rs2416434	1.00[CHB][hapmap]
rs3946989	0.84[CHB][hapmap]
rs4260709	1.00[CHB][hapmap]
rs4301260	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs4484468	1.00[CHB][hapmap]
rs4507525	1.00[CHB][hapmap]
rs4593303	1.00[CHB][hapmap]
rs4921059	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4921076	1.00[CHB][hapmap]
rs4921078	1.00[CHB][hapmap]
rs4921085	0.84[CHB][hapmap]
rs56306460	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57777176	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59583434	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60953939	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62384715	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6594945	0.87[ASN][1000 genomes]
rs6859670	1.00[CHB][hapmap]
rs6866454	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6868145	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6874458	1.00[CHB][hapmap]
rs6874747	0.83[CHB][hapmap]
rs6876214	0.82[CHB][hapmap]
rs6878530	0.84[CHB][hapmap]
rs6878871	1.00[CHB][hapmap]
rs6879075	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6887275	1.00[CHB][hapmap]
rs6887852	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6890263	0.84[CHB][hapmap]
rs6894471	1.00[CHB][hapmap]
rs6898524	0.84[CHB][hapmap]
rs73271270	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7449449	1.00[CHB][hapmap]
rs7701736	0.84[CHB][hapmap]
rs7702152	0.84[CHB][hapmap]
rs7703661	0.82[CHB][hapmap]
rs7703978	0.84[CHB][hapmap]
rs7707191	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7718843	1.00[CHB][hapmap]
rs7719318	1.00[CHB][hapmap]
rs7720518	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7721510	1.00[CHB][hapmap]
rs7723648	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7726794	0.82[CHB][hapmap]
rs7728055	0.84[CHB][hapmap]
rs7730943	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7733187	0.84[CHB][hapmap]
rs7734614	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7736793	0.84[CHB][hapmap]
rs9326997	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs9686231	1.00[CHB][hapmap]
rs9686686	1.00[CHB][hapmap]
rs9687350	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1015976	chr5:115236239-115434163	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv537868	chr5:115236239-115434163	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	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
13	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	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
16	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
20	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10076661	COMMD10	cis	multi-tissue	Pritchard
rs10076661	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs10076661	COMMD10	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115421400-115428800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:115421400-115433400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:115421400-115444200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:115421400-115446400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:115421400-115446400	Weak transcription	Esophagus	oesophagus
6	chr5:115421600-115436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:115421800-115428800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:115421800-115428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:115421800-115448000	Weak transcription	Aorta	Aorta
10	chr5:115422000-115428800	Weak transcription	Fetal Brain Male	brain
11	chr5:115422000-115428800	Weak transcription	Fetal Brain Female	brain
12	chr5:115422000-115428800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:115422000-115433600	Weak transcription	Stomach Mucosa	stomach
14	chr5:115422200-115429000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:115422400-115428800	Weak transcription	Right Ventricle	heart
16	chr5:115422400-115437400	Weak transcription	Spleen	Spleen
17	chr5:115422800-115444200	Weak transcription	Pancreas	Pancrea
18	chr5:115423200-115435000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:115423800-115430800	Strong transcription	Fetal Thymus	thymus
20	chr5:115423800-115431400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:115423800-115431600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr5:115423800-115433400	Strong transcription	HSMM	muscle
23	chr5:115423800-115437000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:115424000-115434600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:115424000-115436400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:115424000-115436600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:115424000-115437000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:115424200-115430800	Strong transcription	Primary B cells from cord blood	blood
29	chr5:115424200-115430800	Strong transcription	Primary T cells from cord blood	blood
30	chr5:115424200-115435200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:115424200-115437000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:115424400-115435400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:115424400-115438800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:115424600-115431000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:115424800-115430800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:115425800-115438400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr5:115426000-115431200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:115426200-115430800	Strong transcription	Fetal Lung	lung
39	chr5:115426200-115436800	Weak transcription	NHEK	skin
40	chr5:115426400-115432400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:115426600-115431200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:115426600-115431200	Strong transcription	HMEC	breast
43	chr5:115426600-115433800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:115426800-115431600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:115426800-115431600	Strong transcription	HUVEC	blood vessel
46	chr5:115426800-115436000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:115427000-115431600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:115427200-115429400	Strong transcription	NHLF	lung
49	chr5:115427200-115430800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:115427200-115430800	Strong transcription	Fetal Intestine Large	intestine

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