Variant report

Variant	rs13028359
Chromosome Location	chr2:20078141-20078142
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	chr2:19988181..19991165-chr2:20075631..20078217,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11886092	0.92[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11888651	0.81[CEU][hapmap];0.85[ASN][1000 genomes]
rs13002069	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35487326	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35946755	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4439914	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666350	0.81[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs893400	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
7	nsv960957	chr2:20076441-20079309	Strong transcription Enhancers Weak transcription Genic enhancers	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13028359	SDC1	cis	parietal	SCAN
rs13028359	PHF17	trans	parietal	SCAN
rs13028359	WDR35	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20086200	Weak transcription	Spleen	Spleen
2	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
3	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
4	chr2:20069400-20078600	Weak transcription	Placenta	Placenta
5	chr2:20069600-20079000	Weak transcription	NHDF-Ad	bronchial
6	chr2:20069600-20079800	Weak transcription	Lung	lung
7	chr2:20069600-20087800	Weak transcription	Gastric	stomach
8	chr2:20069800-20079200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:20070000-20081400	Weak transcription	Esophagus	oesophagus
11	chr2:20071400-20081800	Strong transcription	Primary T cells from cord blood	blood
12	chr2:20071800-20079200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:20072200-20084000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:20074400-20078400	Strong transcription	Fetal Stomach	stomach
15	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
16	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:20076600-20078800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:20076600-20079200	Strong transcription	Fetal Intestine Small	intestine
20	chr2:20076600-20082800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:20076600-20085200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:20076600-20087000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:20076800-20078400	Weak transcription	Thymus	Thymus
26	chr2:20076800-20082000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:20076800-20085600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:20076800-20086000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
30	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
33	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
35	chr2:20077000-20079000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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