Variant report

Variant	rs1048503
Chromosome Location	chr1:228279023-228279024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1034792	0.86[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10495278	1.00[ASW][hapmap]
rs10916262	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10916266	0.81[ASN][1000 genomes]
rs1094603	0.81[ASN][1000 genomes]
rs11577976	1.00[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.84[LWK][hapmap]
rs11582265	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11584499	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11589513	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1188975	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs1188977	1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12033088	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1620734	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1745422	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295995	0.86[EUR][1000 genomes]
rs3738680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3768329	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3795774	0.82[CHB][hapmap]
rs3820624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270175	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41270177	0.84[EUR][1000 genomes]
rs4653533	0.86[JPT][hapmap]
rs4653897	0.84[EUR][1000 genomes]
rs57146523	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57657087	0.81[EUR][1000 genomes]
rs61825130	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61825131	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825133	0.99[ASN][1000 genomes]
rs61825135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825156	0.86[ASN][1000 genomes]
rs708126	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs72756204	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756209	0.81[AMR][1000 genomes]
rs7539664	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs822727	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs860301	1.00[EUR][1000 genomes]
rs882451	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9287011	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1048503	OBSCN	cis	cerebellum	SCAN
rs1048503	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228279400	Genic enhancers	Fetal Muscle Leg	muscle
2	chr1:228272400-228280000	Genic enhancers	Fetal Thymus	thymus
3	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:228272600-228280200	Enhancers	Fetal Heart	heart
5	chr1:228273000-228279200	Genic enhancers	Fetal Intestine Small	intestine
6	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:228273400-228280200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:228273800-228279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:228274000-228279200	Enhancers	Colon Smooth Muscle	Colon
12	chr1:228274000-228280600	Enhancers	Psoas Muscle	Psoas
13	chr1:228274200-228281200	Genic enhancers	Liver	Liver
14	chr1:228274600-228280600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:228274800-228279200	Genic enhancers	Fetal Intestine Large	intestine
16	chr1:228275200-228280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:228275400-228279200	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr1:228275400-228281200	Genic enhancers	Gastric	stomach
20	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr1:228275600-228279200	Genic enhancers	Thymus	Thymus
22	chr1:228275600-228279400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:228275600-228280200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:228275600-228281200	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
27	chr1:228275800-228279800	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:228275800-228280000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:228275800-228280200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:228275800-228281000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
32	chr1:228276000-228280400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:228276000-228281000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:228276000-228281200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:228276000-228281400	Genic enhancers	Placenta	Placenta
36	chr1:228276200-228279400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:228276200-228279800	Genic enhancers	Esophagus	oesophagus
38	chr1:228276200-228280000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:228276200-228280600	Genic enhancers	Osteobl	bone
40	chr1:228276200-228281200	Enhancers	Right Atrium	heart
41	chr1:228276400-228279600	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr1:228276400-228281400	Genic enhancers	Lung	lung
43	chr1:228276600-228280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:228276600-228281200	Genic enhancers	NHEK	skin
45	chr1:228276600-228281800	Weak transcription	Fetal Lung	lung
46	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:228276800-228279400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:228276800-228279600	Genic enhancers	NH-A	brain
49	chr1:228276800-228281200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:228276800-228281800	Weak transcription	H1 Cell Line	embryonic stem cell

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