Variant report

Variant	rs2276677
Chromosome Location	chr2:205990030-205990031
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10196569	0.80[AMR][1000 genomes]
rs10211222	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13429972	0.82[CHB][hapmap]
rs1434160	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289025	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35185167	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4675498	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9678847	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]

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	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1010210	chr2:205489653-206076013	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv16739	chr2:205898770-206127984	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv1000779	chr2:205969138-206064554	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv1009424	chr2:205969138-206078240	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv525418	chr2:205969220-206077607	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv875729	chr2:205972555-206027314	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276677	PARD3B	cis	parietal	SCAN
rs2276677	NIF3L1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205953400-206007200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:205963800-205990200	Weak transcription	Ovary	ovary
3	chr2:205968800-205990200	Weak transcription	Adipose Nuclei	Adipose
4	chr2:205970000-206026000	Weak transcription	HSMMtube	muscle
5	chr2:205973400-205994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:205973400-205998200	Weak transcription	Psoas Muscle	Psoas
7	chr2:205976800-206024400	Weak transcription	Aorta	Aorta
8	chr2:205977000-205990200	Weak transcription	Fetal Intestine Large	intestine
9	chr2:205977200-206000200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:205978800-205990400	Weak transcription	Fetal Lung	lung
11	chr2:205978800-205992200	Weak transcription	Fetal Stomach	stomach
12	chr2:205979400-206014600	Weak transcription	Pancreas	Pancrea
13	chr2:205980600-205990400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:205980600-205994000	Weak transcription	Gastric	stomach
15	chr2:205982400-205997400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:205982600-205994600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:205982600-206003000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:205982800-205992200	Weak transcription	Fetal Intestine Small	intestine
19	chr2:205984600-205998000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:205984800-205992400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:205985000-205992400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:205985000-205992400	Weak transcription	Liver	Liver
23	chr2:205986000-206004400	Weak transcription	Stomach Mucosa	stomach
24	chr2:205988000-205991000	Strong transcription	HSMM	muscle
25	chr2:205988600-205990200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:205989000-206003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:205989200-205990200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:205989200-205991800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:205989400-205992600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:205989600-205991000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:205989800-205991000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:205990000-205990600	Strong transcription	Left Ventricle	heart
33	chr2:205990000-205990800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:205990000-205993600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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