Variant report

Variant	rs338253
Chromosome Location	chr1:58929636-58929637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58928999..58931330-chr1:58934194..58936691,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs338248	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6662936	0.81[EUR][1000 genomes]
rs6666833	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673660	0.80[EUR][1000 genomes]
rs6685601	0.91[ASN][1000 genomes]
rs72669872	0.92[ASN][1000 genomes]
rs72669873	0.94[ASN][1000 genomes]
rs72669875	0.94[ASN][1000 genomes]
rs72669876	0.94[ASN][1000 genomes]
rs72669882	0.91[ASN][1000 genomes]
rs72669887	0.91[ASN][1000 genomes]
rs822062	0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv829948	chr1:58803681-58971380	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv546314	chr1:58915624-58936384	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs338253	TACSTD2	cis	multi-tissue	Pritchard
rs338253	DAB1	cis	cerebellum	SCAN
rs338253	OMA1	cis	parietal	SCAN
rs338253	DAB1	cis	parietal	SCAN
rs338253	OMA1	cis	cerebellum	SCAN
rs338253	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58899000-58934200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:58906200-58932000	Weak transcription	Ovary	ovary
3	chr1:58914000-58930800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:58918400-58974000	Weak transcription	Spleen	Spleen
5	chr1:58920400-58934000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:58921200-58932200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:58923200-58932400	Weak transcription	Fetal Heart	heart
8	chr1:58923200-58954200	Weak transcription	Pancreas	Pancrea
9	chr1:58923400-58932400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:58924000-58932400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:58925000-58942400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:58926400-58932400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:58926400-58942800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:58927400-58934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:58927400-58943200	Weak transcription	Primary B cells from cord blood	blood
16	chr1:58927600-58930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:58928400-58932600	Strong transcription	Primary T cells from cord blood	blood
18	chr1:58928600-58945800	Weak transcription	Aorta	Aorta
19	chr1:58929000-58930200	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:58929000-58954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:58929200-58929800	ZNF genes & repeats	Lung	lung
22	chr1:58929200-58932800	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:58929400-58932200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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