Variant report

Variant	rs1398950
Chromosome Location	chr2:20353356-20353357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20352822..20355874-chr2:20423290..20424865,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11681098	0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11686716	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1398949	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17652287	0.85[ASW][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17697743	0.90[MEX][hapmap]
rs17697993	0.92[CEU][hapmap]
rs55719360	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6531213	0.92[CEU][hapmap]
rs907863	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv581156	chr2:20346312-20356944	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
rs1398950	SDC1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20345600-20356600	Weak transcription	Liver	Liver
3	chr2:20346000-20355600	Weak transcription	Esophagus	oesophagus
4	chr2:20349400-20355400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:20349600-20356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20349800-20353400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:20349800-20355200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:20349800-20355600	Weak transcription	Pancreas	Pancrea
9	chr2:20351000-20356800	Weak transcription	Osteobl	bone
10	chr2:20351200-20353400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:20351200-20353800	Enhancers	GM12878-XiMat	blood
12	chr2:20351200-20356800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:20351200-20357000	Weak transcription	Fetal Lung	lung
14	chr2:20351200-20363800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:20351400-20356800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:20351400-20356800	Weak transcription	HSMM	muscle
17	chr2:20351800-20356600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20352400-20354200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:20352400-20354200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:20352400-20354200	Enhancers	Placenta	Placenta
21	chr2:20352600-20353400	Enhancers	Stomach Mucosa	stomach
22	chr2:20352600-20354200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:20352800-20354200	Enhancers	HMEC	breast
24	chr2:20353000-20353400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:20353000-20353400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:20353000-20353800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:20353200-20353400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:20353200-20353400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:20353200-20353400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:20353200-20353400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:20353200-20353600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:20353200-20353800	Flanking Active TSS	NHEK	skin

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