Variant report

Variant	rs17028771
Chromosome Location	chr2:98306727-98306728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:22)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98279098..98281561-chr2:98304916..98307735,3	MCF-7	breast:
2	chr2:98278665..98281371-chr2:98305087..98308005,4	MCF-7	breast:

(count:22 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.2
2	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.2
3	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.2
4	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
5	lnc-ZAP70-2	chr2:98306719-98306765	NONHSAT072675
6	lnc-ZAP70-2	chr2:98306719-98306765	NONHSAT072676
7	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
8	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
9	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
10	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
11	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
12	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
13	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
14	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
15	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
16	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
17	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
18	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
19	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
20	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5
21	lnc-ZAP70-2	chr2:98306719-98306790	NR_038386
22	lnc-ZAP70-2	chr2:98306719-98306790	ENSG00000228486.5

No data

Variant related genes	Relation type
ENSG00000201806	Chromatin interaction
ENSG00000115073	Chromatin interaction
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17028435	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs17028568	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs17028640	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs17028924	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs17029878	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs17695937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2071038	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290126	0.94[ASN][1000 genomes]
rs2290127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34459720	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35321033	1.00[ASN][1000 genomes]
rs35530168	1.00[ASN][1000 genomes]
rs55757705	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55766309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933640	1.00[ASN][1000 genomes]
rs56035334	1.00[ASN][1000 genomes]
rs56233535	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56717024	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57183691	0.84[AFR][1000 genomes]
rs57875000	0.94[AFR][1000 genomes]
rs58321192	0.94[ASN][1000 genomes]
rs58383658	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59021370	0.94[ASN][1000 genomes]
rs59060391	0.94[ASN][1000 genomes]
rs59168350	1.00[ASN][1000 genomes]
rs62157581	1.00[ASN][1000 genomes]
rs6542982	1.00[ASN][1000 genomes]
rs6753752	1.00[ASN][1000 genomes]
rs72951131	0.94[ASN][1000 genomes]
rs73959772	0.82[AFR][1000 genomes]
rs7425883	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9678135	0.89[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17028771	LOC375249	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98323800	Weak transcription	Gastric	stomach
2	chr2:98292200-98317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98305000-98307600	Weak transcription	HMEC	breast
4	chr2:98305200-98307400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:98305400-98307600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:98305600-98307600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:98305600-98307600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:98305600-98307600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:98305600-98313600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:98306000-98322400	Weak transcription	Fetal Stomach	stomach
11	chr2:98306200-98307800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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