Variant report

Variant	rs549062
Chromosome Location	chr10:97222023-97222024
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	chr10:97220624..97225860-chr10:97227541..97231131,6	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2148892	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274491	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4918930	0.85[ASN][1000 genomes]
rs4918937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533232	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540746	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557941	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7074761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7094140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7899065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs815313	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045002	chr10:97214418-97250630	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3428385	chr10:97221807-97222295	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs549062	PPP1R3C	cis	parietal	SCAN
rs549062	RPL13AP5	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97213200-97234200	Weak transcription	Colonic Mucosa	Colon
2	chr10:97216000-97223000	Weak transcription	Pancreas	Pancrea
3	chr10:97216000-97226800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:97216000-97228200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr10:97217600-97223000	Weak transcription	Placenta	Placenta
6	chr10:97217600-97223000	Weak transcription	Gastric	stomach
7	chr10:97218000-97229600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:97219000-97223200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr10:97219200-97223000	Weak transcription	Lung	lung
10	chr10:97219600-97223000	Weak transcription	HSMMtube	muscle
11	chr10:97219600-97223200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:97219600-97224200	Weak transcription	Stomach Mucosa	stomach
13	chr10:97219600-97225800	Weak transcription	Brain Germinal Matrix	brain
14	chr10:97219800-97222200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:97219800-97222200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:97219800-97222400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr10:97219800-97222400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:97219800-97222600	Weak transcription	Brain Angular Gyrus	brain
19	chr10:97219800-97222600	Weak transcription	Brain Substantia Nigra	brain
20	chr10:97219800-97222600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:97219800-97222800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:97219800-97222800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:97219800-97222800	Weak transcription	Ovary	ovary
24	chr10:97219800-97223000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:97219800-97223400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:97219800-97223400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:97219800-97223600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:97219800-97224400	Weak transcription	Fetal Intestine Small	intestine
29	chr10:97219800-97229600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:97220000-97222400	Weak transcription	Right Ventricle	heart
31	chr10:97220000-97222400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:97220000-97222600	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:97220000-97222600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:97220000-97222800	Enhancers	Fetal Brain Male	brain
35	chr10:97220000-97223000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:97220000-97224200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:97220400-97222800	Weak transcription	Left Ventricle	heart
38	chr10:97220400-97222800	Weak transcription	Right Atrium	heart
39	chr10:97220400-97223400	Weak transcription	Psoas Muscle	Psoas
40	chr10:97220400-97223600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr10:97220600-97222800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr10:97220600-97232000	Enhancers	Fetal Heart	heart
43	chr10:97220800-97222600	Enhancers	Colon Smooth Muscle	Colon
44	chr10:97220800-97225000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr10:97220800-97225000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr10:97221200-97222400	Weak transcription	HepG2	liver
47	chr10:97221200-97222800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr10:97221200-97223000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr10:97221200-97223800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:97221400-97222400	Weak transcription	Brain Hippocampus Middle	brain

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