Variant report

Variant	rs553668
Chromosome Location	chr10:112839579-112839580
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	chr10:112837126..112840004-chr10:112842044..112844644,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10787289	0.83[CHD][hapmap]
rs12241439	0.84[ASN][1000 genomes]
rs12412661	0.81[ASN][1000 genomes]
rs491589	0.96[EUR][1000 genomes]
rs7085088	0.83[ASN][1000 genomes]
rs7090695	0.84[ASN][1000 genomes]
rs7895872	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498045	chr10:112794518-113353550	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv825566	chr10:112830014-112871333	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv527400	chr10:112833561-112843085	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv896004	chr10:112834763-112842961	Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3321787	chr10:112835962-112840760	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv896005	chr10:112835992-112846298	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3377744	chr10:112837487-112840335	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3426722	chr10:112837812-112839710	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs553668	HABP2	cis	parietal	SCAN
rs553668	SMNDC1	cis	parietal	SCAN
rs553668	NRAP	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112835800-112840400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr10:112837200-112839600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr10:112837600-112839600	Bivalent Enhancer	Placenta	Placenta
4	chr10:112838000-112839600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:112838000-112839600	Transcr. at gene 5' and 3'	Pancreas	Pancrea
6	chr10:112838400-112840400	Bivalent Enhancer	Fetal Stomach	stomach
7	chr10:112838400-112847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:112838800-112839800	Bivalent Enhancer	Fetal Intestine Large	intestine
9	chr10:112838800-112839800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr10:112838800-112839800	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr10:112838800-112840200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr10:112839000-112840200	Flanking Active TSS	Ovary	ovary
13	chr10:112839200-112839600	Bivalent Enhancer	Small Intestine	intestine
14	chr10:112839200-112840200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:112839400-112839600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:112839400-112839600	Enhancers	Colonic Mucosa	Colon
17	chr10:112839400-112839600	Flanking Active TSS	Stomach Mucosa	stomach
18	chr10:112839400-112839800	Enhancers	Fetal Brain Male	brain
19	chr10:112839400-112839800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
20	chr10:112839400-112840000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:112839400-112840200	Active TSS	Duodenum Mucosa	Duodenum
22	chr10:112839400-112840200	Bivalent Enhancer	Fetal Intestine Small	intestine
23	chr10:112839400-112840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:112839400-112840400	Bivalent Enhancer	Fetal Lung	lung
25	chr10:112839400-112843400	Weak transcription	Spleen	Spleen
26	chr10:112839400-112848800	Weak transcription	Right Atrium	heart

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