Variant report

Variant	rs1473886
Chromosome Location	chr2:20368519-20368520
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20343897..20346310-chr2:20367652..20370210,2	MCF-7	breast:
2	chr2:20367456..20369768-chr2:20407919..20409910,2	MCF-7	breast:
3	chr2:20362106..20364188-chr2:20366369..20369040,2	MCF-7	breast:
4	chr2:20248476..20251356-chr2:20368246..20369984,2	MCF-7	breast:
5	chr2:20368402..20370917-chr2:20372413..20374946,2	K562	blood:
6	chr2:20366533..20369508-chr2:20380029..20382114,2	MCF-7	breast:
7	chr2:20364675..20367244-chr2:20367416..20369596,2	K562	blood:
8	chr2:20364500..20366851-chr2:20367517..20369898,2	MCF-7	breast:
9	chr2:20347344..20349010-chr2:20367659..20370421,2	MCF-7	breast:

No data

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1107850	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1107851	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1107852	0.82[CHB][hapmap]
rs11096641	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11693335	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11899121	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478327	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13009332	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13010903	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.90[ASN][1000 genomes]
rs2090032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090034	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35135293	0.88[ASN][1000 genomes]
rs6531216	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728072	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7577335	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs870526	0.89[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs870527	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907866	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907867	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907868	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1473886	SDC1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20362400-20371400	Weak transcription	Right Atrium	heart
2	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:20364200-20369200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:20364400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:20364800-20372200	Enhancers	NHEK	skin
6	chr2:20365000-20368600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:20365800-20369800	Weak transcription	Lung	lung
8	chr2:20366000-20369600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr2:20366000-20370400	Weak transcription	Fetal Kidney	kidney
10	chr2:20366000-20370800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:20366000-20371200	Weak transcription	Fetal Lung	lung
12	chr2:20366200-20369000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:20366400-20369200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:20366400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:20366600-20369200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:20366600-20369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:20366600-20371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:20366800-20369400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:20366800-20369800	Weak transcription	Fetal Intestine Small	intestine
20	chr2:20366800-20369800	Weak transcription	HUVEC	blood vessel
21	chr2:20366800-20372600	Enhancers	Placenta	Placenta
22	chr2:20367000-20369200	Enhancers	Colonic Mucosa	Colon
23	chr2:20367200-20369000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:20367200-20376600	Weak transcription	Stomach Mucosa	stomach
25	chr2:20367400-20369400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:20367400-20372200	Weak transcription	GM12878-XiMat	blood
27	chr2:20367600-20368600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:20367600-20368800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:20367600-20369000	Weak transcription	Esophagus	oesophagus
30	chr2:20367600-20369200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:20367600-20369200	Weak transcription	NH-A	brain
32	chr2:20367600-20369800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:20367600-20371200	Weak transcription	Pancreas	Pancrea
34	chr2:20367600-20371200	Weak transcription	HMEC	breast
35	chr2:20367800-20368600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:20367800-20369200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr2:20367800-20369400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:20367800-20369800	Enhancers	Fetal Muscle Leg	muscle
39	chr2:20367800-20383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:20368000-20369000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:20368000-20369800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:20368000-20370600	Enhancers	Brain Germinal Matrix	brain
43	chr2:20368400-20368600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr2:20368400-20368600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr2:20368400-20369800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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