Variant report

Variant	rs34855203
Chromosome Location	chr5:49982011-49982012
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	chr5:49979801..49982370-chr5:49986606..49988193,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10052372	0.86[EUR][1000 genomes]
rs11950506	0.87[EUR][1000 genomes]
rs11952107	1.00[EUR][1000 genomes]
rs11955651	0.94[EUR][1000 genomes]
rs11955934	0.83[EUR][1000 genomes]
rs11959326	0.91[EUR][1000 genomes]
rs13155662	0.87[EUR][1000 genomes]
rs13156735	0.94[EUR][1000 genomes]
rs13157079	0.94[EUR][1000 genomes]
rs13159045	0.81[EUR][1000 genomes]
rs13159239	1.00[EUR][1000 genomes]
rs13161225	0.81[EUR][1000 genomes]
rs13162738	0.94[EUR][1000 genomes]
rs13163470	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163802	0.83[EUR][1000 genomes]
rs13166819	0.81[EUR][1000 genomes]
rs13169153	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13174498	0.94[EUR][1000 genomes]
rs13176737	0.87[EUR][1000 genomes]
rs13181031	0.92[EUR][1000 genomes]
rs13181117	0.94[EUR][1000 genomes]
rs13183910	0.94[EUR][1000 genomes]
rs13186653	0.87[EUR][1000 genomes]
rs13189183	0.81[EUR][1000 genomes]
rs13190144	0.91[EUR][1000 genomes]
rs16886309	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34183555	0.91[EUR][1000 genomes]
rs34264957	0.91[EUR][1000 genomes]
rs34414061	0.96[EUR][1000 genomes]
rs34677483	0.94[EUR][1000 genomes]
rs34758774	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34827507	0.87[EUR][1000 genomes]
rs35128589	1.00[EUR][1000 genomes]
rs35347195	0.87[EUR][1000 genomes]
rs35473824	0.94[EUR][1000 genomes]
rs41270305	0.81[EUR][1000 genomes]
rs6859621	1.00[EUR][1000 genomes]
rs6880398	0.94[EUR][1000 genomes]
rs6883701	0.87[EUR][1000 genomes]
rs6888271	0.87[EUR][1000 genomes]
rs6888315	0.87[EUR][1000 genomes]
rs71615978	1.00[EUR][1000 genomes]
rs71615981	0.94[EUR][1000 genomes]
rs71615983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615984	0.87[EUR][1000 genomes]
rs71615986	0.87[EUR][1000 genomes]
rs71615988	0.81[EUR][1000 genomes]
rs71615990	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71615991	0.81[EUR][1000 genomes]
rs7717073	1.00[EUR][1000 genomes]
rs7726225	1.00[EUR][1000 genomes]
rs7733931	0.94[EUR][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	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34855203	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49964400-49982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:49964400-49983400	Weak transcription	Esophagus	oesophagus
3	chr5:49965800-49983600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:49968800-49990400	Weak transcription	Small Intestine	intestine
5	chr5:49970600-49982600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:49970600-49982600	Weak transcription	Aorta	Aorta
7	chr5:49976200-49985400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr5:49976600-49983600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:49976600-49983600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:49976800-50000000	Weak transcription	Fetal Stomach	stomach
11	chr5:49977600-49983600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:49977800-49990600	Weak transcription	Pancreas	Pancrea
13	chr5:49978200-49985200	Weak transcription	Primary T cells from cord blood	blood
14	chr5:49978200-49995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:49979000-49982600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:49979000-49983400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:49979000-49995200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:49979200-49985600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:49979400-49982600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:49979400-50006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:49979800-49983400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:49980400-49982200	ZNF genes & repeats	Dnd41	blood
23	chr5:49980400-49983400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:49980800-49983200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:49980800-49983200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:49980800-49983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:49980800-49995000	Weak transcription	Thymus	Thymus
28	chr5:49981000-49982600	Weak transcription	Primary B cells from cord blood	blood
29	chr5:49981000-49982600	Weak transcription	Gastric	stomach
30	chr5:49981000-49983400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:49981200-49982600	ZNF genes & repeats	GM12878-XiMat	blood
32	chr5:49981400-49983600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:49981400-49983600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:49981400-49992600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:49981800-49982800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr5:49982000-49982200	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr5:49982000-49982200	Enhancers	Duodenum Mucosa	Duodenum
38	chr5:49982000-49982600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:49982000-49982800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr5:49982000-49982800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:49982000-49982800	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr5:49982000-49984000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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