Variant report

Variant	rs6880398
Chromosome Location	chr5:50032247-50032248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49962390..49964059-chr5:50032146..50034760,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151883	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10052372	0.88[EUR][1000 genomes]
rs11950506	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11952107	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11955651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11955934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11959326	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13153852	0.89[AMR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13156735	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13157079	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13159239	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13161225	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13163470	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13163802	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13166819	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13169153	0.92[EUR][1000 genomes]
rs13169200	1.00[AMR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13176737	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13180485	0.89[AMR][1000 genomes]
rs13181031	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13181117	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13183910	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13186653	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13189183	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13190144	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16886309	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34264957	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34414061	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34443769	1.00[AMR][1000 genomes]
rs34677483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34758774	0.98[EUR][1000 genomes]
rs34827507	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34855203	0.94[EUR][1000 genomes]
rs35128589	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35292338	1.00[AMR][1000 genomes]
rs35347195	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35473824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35596019	1.00[AMR][1000 genomes]
rs41270305	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6883701	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6888271	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6888315	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6892149	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes]
rs71615978	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615981	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615983	0.92[EUR][1000 genomes]
rs71615984	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615990	0.89[EUR][1000 genomes]
rs71615991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71631479	1.00[AMR][1000 genomes]
rs7717073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7726225	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7730188	1.00[AMR][1000 genomes]
rs7733931	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	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
9	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
10	nsv537759	chr5:49986171-50033616	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1030068	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv537760	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv521214	chr5:49988020-50037381	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv462160	chr5:49988020-50058043	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv598109	chr5:49988020-50058043	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv462162	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv598111	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv462164	chr5:50017724-50063035	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv598115	chr5:50017724-50063035	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50014400-50036000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:50023200-50036400	Weak transcription	Pancreas	Pancrea
3	chr5:50023200-50038400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:50023400-50038600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:50023400-50040200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:50024000-50034600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:50024000-50038200	Weak transcription	Primary T cells from cord blood	blood
8	chr5:50024000-50038600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:50024000-50040000	Weak transcription	Small Intestine	intestine
10	chr5:50024200-50032400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:50026600-50038800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:50027000-50040000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:50029200-50034600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:50029600-50032600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:50029600-50033200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr5:50029600-50033800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:50030400-50034800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:50030400-50040000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:50031000-50032400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:50031000-50032400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:50031000-50034000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:50031000-50034000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr5:50031000-50034200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr5:50031200-50032600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr5:50031200-50040200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:50031400-50032600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr5:50031400-50032800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr5:50031400-50032800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:50031400-50033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr5:50031800-50035600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:50031800-50038200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:50032000-50033200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr5:50032000-50034000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:50032000-50034200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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