Variant report

Variant	rs11700515
Chromosome Location	chr21:47379355-47379356
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	chr21:47375803..47379549-chr21:47381128..47384039,3	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11089022	0.82[CEU][hapmap]
rs11700554	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700659	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700719	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700929	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11702443	0.83[CEU][hapmap]
rs11702467	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11702478	0.89[CEU][hapmap]
rs11702503	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11702607	0.83[ASN][1000 genomes]
rs11702616	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11702691	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12627257	0.83[CEU][hapmap]
rs1736419	0.83[EUR][1000 genomes]
rs1736420	0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1736422	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1736423	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1736425	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783075	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs1883047	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070437	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs2075908	0.85[CHB][hapmap]
rs2150459	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2776403	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839027	0.83[CEU][hapmap]
rs2839042	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2839043	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2839045	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs2839046	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2839048	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2839051	0.87[CEU][hapmap]
rs2839052	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2839060	0.85[CHB][hapmap]
rs35314082	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs373617	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs3788219	0.83[CEU][hapmap]
rs379939	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3804036	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs381083	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs386633	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs395418	0.83[EUR][1000 genomes]
rs409280	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs411868	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs413886	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs417745	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs418241	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs418431	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs419348	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs420270	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs431609	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs435299	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs437264	0.90[CHB][hapmap]
rs442400	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs444774	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs446763	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs452332	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs7277877	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278816	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7279643	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7281469	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs7281573	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282661	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283763	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs8128707	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS 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	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
11	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
12	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
14	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
15	nsv914085	chr21:47342116-47433055	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
16	esv1848879	chr21:47343462-47455584	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
17	nsv914086	chr21:47352625-47445184	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
18	nsv914087	chr21:47352625-47453954	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
19	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
20	nsv914088	chr21:47358915-47419012	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
21	esv1846183	chr21:47374343-47389644	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11700515	COL18A1	cis	parietal	SCAN
rs11700515	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47370800-47379600	Weak transcription	Right Ventricle	heart
2	chr21:47377200-47379400	Enhancers	Fetal Lung	lung
3	chr21:47377200-47380000	Enhancers	Adipose Nuclei	Adipose
4	chr21:47377400-47379400	Weak transcription	Aorta	Aorta
5	chr21:47377600-47379600	Enhancers	Fetal Muscle Leg	muscle
6	chr21:47377800-47379400	Enhancers	Fetal Stomach	stomach
7	chr21:47378400-47379400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr21:47378400-47379400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr21:47378600-47379600	Enhancers	Osteobl	bone
10	chr21:47378800-47379400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:47378800-47379600	Weak transcription	Right Atrium	heart
12	chr21:47378800-47380200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:47378800-47380200	Enhancers	NHDF-Ad	bronchial
14	chr21:47378800-47380400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr21:47379000-47379400	Enhancers	Colon Smooth Muscle	Colon
16	chr21:47379000-47379600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr21:47379000-47379800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:47379000-47380200	Enhancers	Ovary	ovary
19	chr21:47379200-47379600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
20	chr21:47379200-47379800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr21:47379200-47379800	Bivalent Enhancer	NHLF	lung
22	chr21:47379200-47380000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr21:47379200-47380000	Enhancers	Left Ventricle	heart
24	chr21:47379200-47380000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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