Variant report

Variant	rs9292197
Chromosome Location	chr5:58501622-58501623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10051456	0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10074426	0.92[CEU][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13155290	0.92[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13173038	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs154222	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs154224	0.92[CEU][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs27172	0.81[CEU][hapmap]
rs27727	0.92[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7724814	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9292198	0.81[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9292197	TPH1	trans	parietal	SCAN
rs9292197	ACTBL2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58485000-58505200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:58485000-58518800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:58485600-58512400	Weak transcription	Pancreas	Pancrea
5	chr5:58485600-58518200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:58486000-58508600	Weak transcription	Fetal Intestine Large	intestine
7	chr5:58490000-58509800	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:58490000-58511600	Weak transcription	Gastric	stomach
9	chr5:58490400-58519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:58491400-58505800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:58491400-58509000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:58491400-58515600	Weak transcription	Fetal Stomach	stomach
13	chr5:58492000-58505600	Weak transcription	Hela-S3	cervix
14	chr5:58492400-58510600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:58494400-58513600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:58494600-58510000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:58496200-58515600	Weak transcription	Fetal Kidney	kidney
18	chr5:58498600-58506200	Weak transcription	Aorta	Aorta
19	chr5:58498800-58501800	Genic enhancers	A549	lung
20	chr5:58500200-58503200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr5:58500200-58503600	Enhancers	Colon Smooth Muscle	Colon
22	chr5:58500200-58506400	Enhancers	Rectal Smooth Muscle	rectum
23	chr5:58500400-58502400	Enhancers	Stomach Smooth Muscle	stomach
24	chr5:58500400-58503000	Enhancers	Psoas Muscle	Psoas
25	chr5:58500800-58502200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr5:58500800-58502400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:58500800-58503000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:58500800-58503000	Enhancers	Right Atrium	heart
29	chr5:58500800-58503200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:58500800-58503400	Enhancers	Osteobl	bone
31	chr5:58501000-58503000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:58501200-58501800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr5:58501200-58502400	Enhancers	Fetal Heart	heart
34	chr5:58501200-58503600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:58501400-58502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:58501400-58502600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:58501400-58502800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:58501600-58502200	Enhancers	Fetal Lung	lung
39	chr5:58501600-58502400	Enhancers	HSMMtube	muscle
40	chr5:58501600-58502600	Weak transcription	Left Ventricle	heart
41	chr5:58501600-58502600	Weak transcription	Right Ventricle	heart
42	chr5:58501600-58502600	Enhancers	HSMM	muscle
43	chr5:58501600-58503000	Enhancers	NH-A	brain
44	chr5:58501600-58503200	Enhancers	HUVEC	blood vessel

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