Variant report

Variant	rs2294195
Chromosome Location	chr1:166838281-166838282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POGK-1	chr1:166837985-166838446	NONHSAT007368

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10800270	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800276	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918600	0.82[CEU][hapmap];0.90[TSI][hapmap]
rs10918603	0.80[TSI][hapmap]
rs11576455	0.89[EUR][1000 genomes]
rs11579987	0.82[CEU][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs11583927	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11584352	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12062326	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12562794	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1476347	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1543313	0.97[ASN][1000 genomes]
rs2072740	0.96[ASN][1000 genomes]
rs2075946	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2142615	0.82[CEU][hapmap]
rs2223221	0.93[ASN][1000 genomes]
rs2235184	0.88[CEU][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2280995	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34381372	0.95[ASN][1000 genomes]
rs3820387	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4656516	0.95[ASN][1000 genomes]
rs4657609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4657612	0.93[ASN][1000 genomes]
rs4657613	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56229522	0.82[ASN][1000 genomes]
rs6427047	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs742048	0.82[CEU][hapmap];0.90[TSI][hapmap]
rs7513457	0.93[ASN][1000 genomes]
rs7545806	0.80[TSI][hapmap]
rs9633326	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2294195	B4GALT3	cis	parietal	SCAN
rs2294195	RGS4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166809600-166844400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:166810600-166838800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:166810800-166839200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:166810800-166839200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:166811200-166839800	Strong transcription	Primary T cells from cord blood	blood
6	chr1:166811800-166838600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:166811800-166838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:166812000-166838400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:166812000-166838800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:166812200-166838800	Strong transcription	Fetal Thymus	thymus
11	chr1:166813200-166840600	Strong transcription	Dnd41	blood
12	chr1:166813400-166838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:166813600-166838600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:166813600-166839200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:166813800-166838400	Strong transcription	Fetal Intestine Large	intestine
16	chr1:166814200-166838800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:166815200-166838400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:166819400-166841400	Weak transcription	Stomach Mucosa	stomach
19	chr1:166819600-166838400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:166819800-166842600	Weak transcription	Small Intestine	intestine
21	chr1:166825000-166844400	Weak transcription	HSMMtube	muscle
22	chr1:166825600-166839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:166825800-166838800	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:166827000-166840800	Weak transcription	Psoas Muscle	Psoas
25	chr1:166828600-166838400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:166829200-166838400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:166829200-166843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:166829200-166844200	Weak transcription	Fetal Heart	heart
29	chr1:166829200-166844400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:166829400-166840600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:166831000-166841400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:166831200-166838400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:166831600-166838600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr1:166831600-166838600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:166831600-166839200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:166831600-166841800	Weak transcription	Esophagus	oesophagus
37	chr1:166831600-166844600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:166831800-166839200	Weak transcription	Brain Angular Gyrus	brain
39	chr1:166831800-166844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:166831800-166844400	Weak transcription	Fetal Kidney	kidney
41	chr1:166832400-166838600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:166833200-166838400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:166833800-166838400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:166833800-166839200	Weak transcription	Pancreas	Pancrea
45	chr1:166834000-166839200	Weak transcription	Ovary	ovary
46	chr1:166834200-166843800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:166834200-166844800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:166835000-166838800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:166835200-166838400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:166835400-166841200	Weak transcription	Right Atrium	heart

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