Variant report

Variant	rs1016028
Chromosome Location	chr7:7557297-7557298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:103022096..103022829-chr7:7557065..7557847,2	MCF-7	breast:
2	chr7:7556776..7558526-chr7:7562736..7564916,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPA3-4	chr7:7556936-7557632	l_3359_chr7:7556673-7558351_thyroid

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1013002	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10229961	0.81[EUR][1000 genomes]
rs10276434	0.81[EUR][1000 genomes]
rs11773679	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11976831	1.00[EUR][1000 genomes]
rs11983756	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12535954	0.86[EUR][1000 genomes]
rs17167064	1.00[GIH][hapmap]
rs1978189	0.86[MKK][hapmap]
rs2006880	0.92[AFR][1000 genomes]
rs2051910	0.86[EUR][1000 genomes]
rs2051912	0.86[EUR][1000 genomes]
rs2051913	0.86[EUR][1000 genomes]
rs2051914	0.86[EUR][1000 genomes]
rs2108063	0.81[EUR][1000 genomes]
rs2108064	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2108067	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2190248	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2348265	0.86[EUR][1000 genomes]
rs2348336	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2348339	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2881888	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2881890	0.81[EUR][1000 genomes]
rs3757532	1.00[CEU][hapmap];0.90[MKK][hapmap]
rs4035104	0.86[EUR][1000 genomes]
rs4380838	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4720739	0.80[AFR][1000 genomes]
rs4720741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4725005	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs6463696	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6463702	1.00[CEU][hapmap]
rs6463705	0.86[EUR][1000 genomes]
rs6946022	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6946425	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6948157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6948448	0.91[EUR][1000 genomes]
rs6957976	1.00[CEU][hapmap]
rs6958110	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6962939	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6964397	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6974246	0.86[EUR][1000 genomes]
rs7384200	0.81[EUR][1000 genomes]
rs7783239	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7789187	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7789287	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7791344	0.95[EUR][1000 genomes]
rs7791808	0.82[CEU][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs7796709	1.00[EUR][1000 genomes]
rs7804532	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs7805565	0.86[EUR][1000 genomes]
rs7806046	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7808788	1.00[EUR][1000 genomes]
rs7810367	0.86[EUR][1000 genomes]
rs9640043	1.00[EUR][1000 genomes]
rs9640044	0.86[EUR][1000 genomes]
rs9640045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs972600	1.00[EUR][1000 genomes]
rs974320	0.82[CEU][hapmap];0.90[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv606043	chr7:7473563-7571420	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
18	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7528600-7575400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7529000-7557600	Weak transcription	Pancreas	Pancrea
3	chr7:7551200-7563000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:7551800-7561200	Weak transcription	Placenta	Placenta
5	chr7:7553600-7563200	Weak transcription	Osteobl	bone
6	chr7:7554600-7560200	Weak transcription	Small Intestine	intestine
7	chr7:7555200-7558400	Enhancers	HepG2	liver
8	chr7:7555600-7557800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr7:7555600-7558200	Enhancers	Fetal Intestine Small	intestine
10	chr7:7555800-7557800	Enhancers	Fetal Intestine Large	intestine
11	chr7:7555800-7561200	Enhancers	A549	lung
12	chr7:7556000-7557600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr7:7556000-7558200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:7556000-7558800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:7556600-7558000	Enhancers	Hela-S3	cervix
16	chr7:7556800-7558000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:7557000-7557400	Enhancers	Duodenum Mucosa	Duodenum
18	chr7:7557200-7557400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:7557200-7557800	Enhancers	Stomach Mucosa	stomach
20	chr7:7557200-7557800	Enhancers	NHLF	lung
21	chr7:7557200-7558000	Enhancers	Fetal Kidney	kidney
22	chr7:7557200-7558000	Enhancers	NHDF-Ad	bronchial

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