Variant report

Variant	rs6975312
Chromosome Location	chr7:50620030-50620031
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10499693	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575293	1.00[EUR][1000 genomes]
rs11575302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575340	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575343	1.00[EUR][1000 genomes]
rs11575360	1.00[EUR][1000 genomes]
rs11575381	1.00[EUR][1000 genomes]
rs11575385	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575407	1.00[EUR][1000 genomes]
rs11575447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575493	1.00[EUR][1000 genomes]
rs11575494	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575501	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575502	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575503	1.00[EUR][1000 genomes]
rs11575504	1.00[EUR][1000 genomes]
rs11575505	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575507	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575508	1.00[EUR][1000 genomes]
rs11575510	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575511	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575512	1.00[EUR][1000 genomes]
rs11575514	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575518	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575519	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575522	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575523	1.00[EUR][1000 genomes]
rs11575527	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575535	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575537	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575540	1.00[EUR][1000 genomes]
rs11575542	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575543	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575546	1.00[EUR][1000 genomes]
rs11575547	1.00[EUR][1000 genomes]
rs11575549	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11978797	0.92[EUR][1000 genomes]
rs11981575	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11982708	1.00[EUR][1000 genomes]
rs11982772	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11982776	0.92[EUR][1000 genomes]
rs11983581	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11983757	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12112308	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12113897	0.84[EUR][1000 genomes]
rs2329370	1.00[EUR][1000 genomes]
rs3173669	0.92[EUR][1000 genomes]
rs55869201	1.00[EUR][1000 genomes]
rs55992615	1.00[EUR][1000 genomes]
rs56030652	1.00[EUR][1000 genomes]
rs57167849	0.92[EUR][1000 genomes]
rs57835901	1.00[EUR][1000 genomes]
rs59150746	1.00[EUR][1000 genomes]
rs59828622	0.92[EUR][1000 genomes]
rs6956737	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6978556	0.92[EUR][1000 genomes]
rs73695512	1.00[EUR][1000 genomes]
rs73695638	0.84[EUR][1000 genomes]
rs73695639	0.92[EUR][1000 genomes]
rs73695640	0.92[EUR][1000 genomes]
rs73695641	0.92[EUR][1000 genomes]
rs73695643	0.92[EUR][1000 genomes]
rs73695661	0.92[EUR][1000 genomes]
rs73695664	0.92[EUR][1000 genomes]
rs73695666	0.92[EUR][1000 genomes]
rs73695667	0.92[EUR][1000 genomes]
rs73695668	0.92[EUR][1000 genomes]
rs73695669	0.92[EUR][1000 genomes]
rs73695670	0.92[EUR][1000 genomes]
rs73695671	0.92[EUR][1000 genomes]
rs73695672	0.92[EUR][1000 genomes]
rs73695673	0.92[EUR][1000 genomes]
rs73695681	1.00[EUR][1000 genomes]
rs73695682	1.00[EUR][1000 genomes]
rs73695683	1.00[EUR][1000 genomes]
rs73695684	1.00[EUR][1000 genomes]
rs73695700	1.00[EUR][1000 genomes]
rs73695701	1.00[EUR][1000 genomes]
rs73695702	1.00[EUR][1000 genomes]
rs73697528	1.00[EUR][1000 genomes]
rs73697574	1.00[EUR][1000 genomes]
rs930707	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9942578	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6975312	IKZF1	cis	lymphoblastoid	seeQTL
rs6975312	GRK5	trans	brain	seeQTL
rs6975312	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:50611000-50631800	Weak transcription	Colonic Mucosa	Colon
3	chr7:50611600-50623800	Weak transcription	Liver	Liver
4	chr7:50613000-50621600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:50619400-50620600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:50619400-50624400	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50619400-50628200	Enhancers	HepG2	liver
8	chr7:50619600-50620600	Enhancers	Stomach Mucosa	stomach
9	chr7:50619600-50621000	Enhancers	Gastric	stomach
10	chr7:50619600-50627800	Enhancers	Fetal Intestine Large	intestine
11	chr7:50620000-50620200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:50620000-50620800	Enhancers	Esophagus	oesophagus
13	chr7:50620000-50620800	Enhancers	Lung	lung
14	chr7:50620000-50621000	Enhancers	Pancreas	Pancrea

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