Variant report

Variant	rs1890850
Chromosome Location	chr1:78641967-78641968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1022103	0.86[ASW][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10873966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11162415	0.93[ASN][1000 genomes]
rs11162417	0.88[ASN][1000 genomes]
rs11162425	0.99[ASN][1000 genomes]
rs11162429	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579434	0.93[ASN][1000 genomes]
rs12095545	0.99[ASN][1000 genomes]
rs12123953	0.80[LWK][hapmap]
rs12184300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12758374	0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1323094	1.00[ASN][1000 genomes]
rs2146612	0.96[ASN][1000 genomes]
rs2208966	0.99[ASN][1000 genomes]
rs4650382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4650619	0.90[ASN][1000 genomes]
rs4650620	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs616518	1.00[ASN][1000 genomes]
rs638232	0.96[ASN][1000 genomes]
rs640124	0.97[ASN][1000 genomes]
rs653899	1.00[ASN][1000 genomes]
rs689374	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7524877	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1000388	chr1:78638946-78665285	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv520237	chr1:78639244-78660123	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1890850	TNNI3K	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78638600-78642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:78638800-78642000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:78638800-78642000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:78641600-78642800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:78641600-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:78641600-78643400	Enhancers	Fetal Muscle Leg	muscle
9	chr1:78641600-78643800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:78641800-78642200	Enhancers	HSMM	muscle
11	chr1:78641800-78642400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:78641800-78642600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:78641800-78642600	Enhancers	HMEC	breast
14	chr1:78641800-78642600	Enhancers	NHEK	skin
15	chr1:78641800-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:78641800-78643200	Enhancers	Osteobl	bone
17	chr1:78641800-78643800	Enhancers	NHDF-Ad	bronchial
18	chr1:78641800-78645200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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