Variant report

Variant	rs3807553
Chromosome Location	chr7:50610613-50610614
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	chr7:50605928..50607774-chr7:50609469..50611799,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IKZF1-1	chr7:50609943-50611161	ENSG00000226122.1

Variant related genes	Relation type
ENSG00000132437	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10268819	1.00[JPT][hapmap]
rs1037350	0.87[ASN][1000 genomes]
rs10499691	0.87[ASN][1000 genomes]
rs10499696	1.00[JPT][hapmap]
rs1107742	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1107743	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11575282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11575286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11575298	1.00[JPT][hapmap]
rs11575313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575342	1.00[JPT][hapmap]
rs11575349	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575404	1.00[JPT][hapmap]
rs11575410	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11575442	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11575521	0.93[ASN][1000 genomes]
rs11575548	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11575553	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11575562	0.87[ASN][1000 genomes]
rs11771818	1.00[JPT][hapmap]
rs11976368	0.87[ASN][1000 genomes]
rs11978591	0.87[ASN][1000 genomes]
rs1349491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466163	1.00[JPT][hapmap]
rs1470748	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17133817	0.87[ASN][1000 genomes]
rs17133826	0.87[ASN][1000 genomes]
rs17553036	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17553791	1.00[JPT][hapmap]
rs17634476	0.87[ASN][1000 genomes]
rs17634717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17634771	1.00[JPT][hapmap]
rs17634958	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17635123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2100279	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122817	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242041	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2329367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2329369	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2715126	1.00[JPT][hapmap]
rs2876826	0.87[ASN][1000 genomes]
rs2876830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3177656	1.00[JPT][hapmap]
rs3735271	0.82[EUR][1000 genomes]
rs3779081	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779084	0.82[CHB][hapmap]
rs3807550	1.00[ASW][hapmap];0.80[CHB][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3807551	1.00[ASW][hapmap];0.80[CHB][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4469405	0.82[EUR][1000 genomes]
rs4585697	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs4602840	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4947710	0.80[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs55834323	0.82[EUR][1000 genomes]
rs56056130	0.87[ASN][1000 genomes]
rs56670620	0.85[EUR][1000 genomes]
rs58129743	0.85[EUR][1000 genomes]
rs67275148	0.85[EUR][1000 genomes]
rs6944090	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs6959427	0.82[ASN][1000 genomes]
rs71018475	0.85[ASN][1000 genomes]
rs73117270	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73119230	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73119239	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73119245	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73119251	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73121271	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73121282	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73121285	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73121287	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73121290	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73121292	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73123220	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123247	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123249	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123251	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123254	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123257	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123261	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123264	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123266	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73123285	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73123291	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73125208	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73125215	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73125225	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73129082	0.82[EUR][1000 genomes]
rs73129084	0.82[EUR][1000 genomes]
rs73129088	0.82[EUR][1000 genomes]
rs73129091	0.82[EUR][1000 genomes]
rs73129096	0.82[EUR][1000 genomes]
rs73131006	0.82[EUR][1000 genomes]
rs73131008	0.82[EUR][1000 genomes]
rs73131013	0.82[EUR][1000 genomes]
rs73131078	0.82[EUR][1000 genomes]
rs73695642	0.87[ASN][1000 genomes]
rs73695660	0.87[ASN][1000 genomes]
rs73695663	0.87[ASN][1000 genomes]
rs7777600	0.90[CHB][hapmap];0.92[CHD][hapmap];0.91[ASN][1000 genomes]
rs880028	0.82[CHB][hapmap]
rs896308	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9656664	0.80[CHB][hapmap];0.80[GIH][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv429750	chr7:50603534-50622712	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv429752	chr7:50607353-50620030	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv429751	chr7:50607353-50622712	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50600200-50612600	Weak transcription	Small Intestine	intestine
2	chr7:50600600-50619400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:50602600-50618200	Weak transcription	Pancreas	Pancrea
5	chr7:50602800-50613800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:50603600-50613000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr7:50604000-50612000	Strong transcription	Fetal Intestine Large	intestine
8	chr7:50604400-50612000	Strong transcription	HepG2	liver
9	chr7:50604600-50612400	Strong transcription	Fetal Intestine Small	intestine
10	chr7:50607000-50612000	Weak transcription	Fetal Stomach	stomach
11	chr7:50609000-50611800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr7:50609600-50611600	Strong transcription	Liver	Liver
13	chr7:50610000-50611200	Weak transcription	Stomach Mucosa	stomach
14	chr7:50610200-50611000	Strong transcription	Colonic Mucosa	Colon
15	chr7:50610200-50611000	Enhancers	Placenta	Placenta
16	chr7:50610600-50611000	Weak transcription	Spleen	Spleen

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