Variant report

Variant	rs28711235
Chromosome Location	chr5:50030383-50030384
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	chr5:49986640..49989197-chr5:50027826..50030637,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10035164	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10036060	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10039272	1.00[ASN][1000 genomes]
rs10044566	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10051561	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10054381	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10056836	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10058388	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10059085	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10060850	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10065432	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10072398	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10075034	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10085036	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10755235	0.81[ASN][1000 genomes]
rs10940472	0.88[ASN][1000 genomes]
rs10940497	0.88[ASN][1000 genomes]
rs11750241	0.88[ASN][1000 genomes]
rs11750771	0.88[ASN][1000 genomes]
rs12188262	0.88[ASN][1000 genomes]
rs12188654	0.84[ASN][1000 genomes]
rs12519006	0.80[ASN][1000 genomes]
rs12521579	0.80[ASN][1000 genomes]
rs13153982	0.88[ASN][1000 genomes]
rs13173734	0.88[ASN][1000 genomes]
rs13359044	0.80[ASN][1000 genomes]
rs13361410	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13436520	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs152102	0.80[ASN][1000 genomes]
rs154134	0.80[ASN][1000 genomes]
rs154135	0.80[ASN][1000 genomes]
rs154137	0.80[ASN][1000 genomes]
rs154138	0.80[ASN][1000 genomes]
rs154140	0.80[ASN][1000 genomes]
rs154141	0.80[ASN][1000 genomes]
rs16884018	0.84[ASN][1000 genomes]
rs169497	0.80[ASN][1000 genomes]
rs17195388	0.80[ASN][1000 genomes]
rs182230	0.88[ASN][1000 genomes]
rs2354525	0.87[ASN][1000 genomes]
rs2548581	0.80[ASN][1000 genomes]
rs2548582	0.80[ASN][1000 genomes]
rs256341	0.80[ASN][1000 genomes]
rs2594706	0.88[ASN][1000 genomes]
rs26062	0.80[ASN][1000 genomes]
rs26065	0.80[ASN][1000 genomes]
rs26069	0.80[ASN][1000 genomes]
rs26071	0.80[ASN][1000 genomes]
rs27254	0.80[ASN][1000 genomes]
rs27357	0.80[ASN][1000 genomes]
rs27465	0.80[ASN][1000 genomes]
rs27468	0.80[ASN][1000 genomes]
rs27469	0.80[ASN][1000 genomes]
rs27627	0.80[ASN][1000 genomes]
rs282550	0.80[ASN][1000 genomes]
rs282551	0.80[ASN][1000 genomes]
rs282552	0.80[ASN][1000 genomes]
rs282553	0.88[ASN][1000 genomes]
rs282557	0.88[ASN][1000 genomes]
rs282561	0.88[ASN][1000 genomes]
rs28505342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs32376	0.80[ASN][1000 genomes]
rs32404	0.91[ASN][1000 genomes]
rs32425	0.80[ASN][1000 genomes]
rs3763367	0.84[ASN][1000 genomes]
rs39613	0.80[ASN][1000 genomes]
rs39949	0.80[ASN][1000 genomes]
rs42284	0.80[ASN][1000 genomes]
rs4865628	0.88[ASN][1000 genomes]
rs57079776	0.84[ASN][1000 genomes]
rs62366937	0.88[ASN][1000 genomes]
rs6872496	0.88[ASN][1000 genomes]
rs6890519	0.88[ASN][1000 genomes]
rs73097023	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73101028	0.88[ASN][1000 genomes]
rs73101075	0.91[ASN][1000 genomes]
rs7728126	0.82[ASN][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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50007800-50031000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:50014400-50036000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:50023200-50036400	Weak transcription	Pancreas	Pancrea
4	chr5:50023200-50038400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:50023400-50038600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:50023400-50040200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:50024000-50034600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:50024000-50038200	Weak transcription	Primary T cells from cord blood	blood
9	chr5:50024000-50038600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:50024000-50040000	Weak transcription	Small Intestine	intestine
11	chr5:50024200-50032400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:50025200-50031000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:50025400-50032000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:50025800-50031000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:50026200-50031000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:50026400-50031200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:50026600-50038800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:50027000-50031000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:50027000-50031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:50027000-50031400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:50027000-50040000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:50029200-50034600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:50029600-50030400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr5:50029600-50032600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:50029600-50033200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr5:50029600-50033800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:50030000-50030400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:50030000-50031000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:50030200-50031000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:50030200-50031000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:50030200-50031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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