Variant report

Variant	rs6805339
Chromosome Location	chr3:111602770-111602771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10934118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934119	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10934121	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10934122	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934123	0.90[YRI][hapmap]
rs11922171	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13064071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065448	0.83[CHB][hapmap]
rs13070728	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1500045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1500046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1587455	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2055364	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682322	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682323	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6438021	0.90[YRI][hapmap]
rs6767186	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775272	0.81[ASN][1000 genomes]
rs6781879	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784285	0.90[YRI][hapmap]
rs6785402	0.80[ASN][1000 genomes]
rs6786077	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6789911	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796290	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6805359	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7621455	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7621473	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7640094	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7649418	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6805339	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
6	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
8	chr3:111591600-111603200	Weak transcription	Ovary	ovary
9	chr3:111591600-111603600	Weak transcription	HepG2	liver
10	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
12	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:111593600-111603000	Weak transcription	Lung	lung
14	chr3:111593600-111603200	Weak transcription	Gastric	stomach
15	chr3:111593600-111603400	Weak transcription	HSMM	muscle
16	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:111593800-111602800	Weak transcription	NHLF	lung
18	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
19	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:111593800-111603400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:111594000-111603400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:111594400-111603200	Weak transcription	HMEC	breast
23	chr3:111598400-111612600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:111599200-111603400	Weak transcription	Right Atrium	heart
25	chr3:111599400-111603600	Weak transcription	NH-A	brain
26	chr3:111599600-111603000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:111599600-111603000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:111600200-111602800	Weak transcription	Liver	Liver
29	chr3:111600200-111603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:111600200-111603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:111600200-111604000	Weak transcription	A549	lung
32	chr3:111600400-111603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:111600400-111603400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:111600400-111603600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:111600600-111603000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:111600600-111603000	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:111600600-111603200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:111600600-111603200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:111600600-111603400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:111601200-111602800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:111601200-111603200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:111601200-111612400	Strong transcription	NHEK	skin
43	chr3:111601400-111603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:111601600-111603000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:111601600-111603000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:111601600-111603000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:111601600-111603000	Weak transcription	Aorta	Aorta
48	chr3:111601600-111603000	Weak transcription	Osteobl	bone
49	chr3:111601600-111603200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:111601600-111603200	Weak transcription	Stomach Smooth Muscle	stomach

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