Variant report

Variant	rs7809234
Chromosome Location	chr7:50610379-50610380
allele	A/T
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: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10268819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575300	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575301	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575404	1.00[ASN][1000 genomes]
rs11575429	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11765109	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770199	1.00[CHB][hapmap]
rs11771818	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs11772525	1.00[CHB][hapmap]
rs12718611	0.85[EUR][1000 genomes]
rs1466163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553791	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17634771	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2167368	1.00[ASN][1000 genomes]
rs2329486	1.00[CHB][hapmap]
rs2715129	1.00[CHB][hapmap]
rs4947714	1.00[CHB][hapmap]
rs6593002	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944090	1.00[JPT][hapmap]
rs6952381	1.00[ASN][1000 genomes]
rs6975015	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975747	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73342846	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777600	1.00[JPT][hapmap]
rs7785984	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810039	1.00[CHB][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite ratios	24816252	GWAS catalog

Chromatin state (count:17 , 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	chr7:50610000-50610400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:50610000-50611200	Weak transcription	Stomach Mucosa	stomach
15	chr7:50610200-50610600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:50610200-50611000	Strong transcription	Colonic Mucosa	Colon
17	chr7:50610200-50611000	Enhancers	Placenta	Placenta

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