Variant report

Variant	rs11982489
Chromosome Location	chr7:26722483-26722484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26721768..26723951-chr7:27183878..27185970,2	MCF-7	breast:
2	chr7:26721606..26723393-chr7:27184950..27187202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254369	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1024452	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024453	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129771	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971041	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971098	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972823	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973332	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976472	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978456	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979611	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57579189	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57687803	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61609910	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945204	0.85[EUR][1000 genomes]
rs6967749	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970475	1.00[ASN][1000 genomes]
rs73683491	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683496	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683510	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777645	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780206	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799519	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809419	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1020378	chr7:26679880-26733872	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv5672	chr7:26711462-26757891	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11982489	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26705000-26759600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:26708800-26725600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:26715000-26731200	Weak transcription	Lung	lung
4	chr7:26715600-26724600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:26715600-26725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:26715600-26725200	Weak transcription	NHEK	skin
7	chr7:26715600-26725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:26715600-26726000	Weak transcription	Osteobl	bone
9	chr7:26715600-26726200	Weak transcription	HMEC	breast
10	chr7:26716400-26726000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:26716400-26728200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:26716800-26723000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:26716800-26729200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:26718200-26722800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:26719200-26724200	Weak transcription	Primary B cells from cord blood	blood
16	chr7:26720800-26728600	Weak transcription	Spleen	Spleen
17	chr7:26721000-26724600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:26721000-26726000	Weak transcription	Fetal Intestine Large	intestine
19	chr7:26721000-26726200	Weak transcription	Fetal Intestine Small	intestine
20	chr7:26721200-26726000	Weak transcription	HepG2	liver
21	chr7:26721600-26724800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:26721600-26725000	Enhancers	HUVEC	blood vessel
23	chr7:26721800-26722600	Enhancers	Adipose Nuclei	Adipose
24	chr7:26721800-26722800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:26721800-26724400	Bivalent Enhancer	Fetal Lung	lung
26	chr7:26722000-26722600	Enhancers	Duodenum Mucosa	Duodenum
27	chr7:26722200-26726400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:26722200-26728800	Weak transcription	Small Intestine	intestine
29	chr7:26722400-26724200	Weak transcription	Stomach Mucosa	stomach
30	chr7:26722400-26724400	Strong transcription	Primary monocytes fromperipheralblood	blood

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