Variant report

Variant	rs34405528
Chromosome Location	chr2:46667351-46667352
allele	C/T
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:1)
LncRNA
region (count:13)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46661749..46663696-chr2:46665776..46668520,2	MCF-7	breast:

(count:13 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
2	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
3	lnc-AC018682.6.1-1	chr2:46667270-46667365	XLOC_001455
4	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
5	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
6	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
7	lnc-AC018682.6.1-1	chr2:46667266-46667434	XLOC_001455
8	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
9	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
10	lnc-AC018682.6.1-1	chr2:46667266-46667365	XLOC_001455
11	lnc-AC018682.6.1-1	chr2:46667266-46667365	NONHSAT070496
12	lnc-AC018682.6.1-1	chr2:46667266-46667365	NONHSAT070498
13	lnc-AC018682.6.1-1	chr2:46667266-46667365	NONHSAT147087

No data

Variant related genes	Relation type
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1105595	0.80[ASN][1000 genomes]
rs11125078	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12470939	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12471274	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472120	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12473673	0.83[EUR][1000 genomes]
rs12474961	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474965	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475015	0.97[ASN][1000 genomes]
rs12613088	0.81[ASN][1000 genomes]
rs12617193	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12619386	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619696	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619754	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621486	0.84[EUR][1000 genomes]
rs12622818	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530623	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1551123	0.86[EUR][1000 genomes]
rs1562454	0.86[EUR][1000 genomes]
rs17035200	0.83[EUR][1000 genomes]
rs1868090	0.83[ASN][1000 genomes]
rs1868095	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868845	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053766	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2121699	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2166746	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276556	0.83[EUR][1000 genomes]
rs2881326	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35589072	0.83[EUR][1000 genomes]
rs4145835	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952826	0.83[EUR][1000 genomes]
rs4952827	0.83[EUR][1000 genomes]
rs4953364	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953369	0.83[ASN][1000 genomes]
rs4953370	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953376	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4953395	0.83[EUR][1000 genomes]
rs55871716	0.83[EUR][1000 genomes]
rs56894248	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57720200	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57996107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58402726	0.80[EUR][1000 genomes]
rs58725320	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59013670	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59761895	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59856996	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60685999	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61193538	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61560601	0.87[ASN][1000 genomes]
rs66533451	0.83[EUR][1000 genomes]
rs6714240	0.80[EUR][1000 genomes]
rs6723195	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67435514	0.84[ASN][1000 genomes]
rs67739992	0.83[EUR][1000 genomes]
rs67960524	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68030749	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72618620	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72618621	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72618622	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618623	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72618624	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618625	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618626	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72618627	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72618628	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72618629	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72618631	0.83[EUR][1000 genomes]
rs72618632	0.80[EUR][1000 genomes]
rs72873772	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7573688	0.80[EUR][1000 genomes]
rs7574467	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7595513	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1001902	chr2:46651624-46675665	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997637	chr2:46651624-46676628	Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1003646	chr2:46651624-46677186	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS 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
10	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv581745	chr2:46660445-46693963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46657200-46672200	Enhancers	HepG2	liver
2	chr2:46660800-46669600	Weak transcription	Pancreas	Pancrea
3	chr2:46662200-46678400	Weak transcription	Placenta	Placenta
4	chr2:46663200-46671400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:46665200-46668400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:46665400-46668200	Enhancers	K562	blood
7	chr2:46665400-46668400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:46665600-46668000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:46665600-46668600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:46665800-46668000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:46665800-46668000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:46665800-46668000	Enhancers	Dnd41	blood
13	chr2:46665800-46668200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:46665800-46668600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:46666200-46667800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:46666200-46668000	Enhancers	Thymus	Thymus
17	chr2:46666200-46668200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:46666200-46668200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:46666400-46668200	Enhancers	Fetal Thymus	thymus
20	chr2:46666600-46667400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr2:46666600-46667600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:46667000-46667400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:46667000-46667800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:46667200-46667400	Flanking Active TSS	Primary T cells from cord blood	blood

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