Variant report

Variant	rs1000199
Chromosome Location	chr3:119113762-119113763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001674	0.94[ASN][1000 genomes]
rs10511391	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12485665	0.81[ASN][1000 genomes]
rs12487191	0.87[ASN][1000 genomes]
rs12487982	0.87[ASN][1000 genomes]
rs12488164	0.81[ASN][1000 genomes]
rs12489912	0.87[ASN][1000 genomes]
rs12490630	0.87[ASN][1000 genomes]
rs12492315	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12492609	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12492859	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12493175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12493326	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12493328	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12493965	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12494943	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12495539	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12495580	0.84[ASN][1000 genomes]
rs12495749	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.87[ASN][1000 genomes]
rs12496277	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12497394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13062955	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13078312	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13081067	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13081197	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13090653	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13094625	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13096213	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs16829838	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16829850	0.84[ASN][1000 genomes]
rs16829853	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1997341	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2121994	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282170	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs34023538	0.87[ASN][1000 genomes]
rs34208844	0.83[ASN][1000 genomes]
rs34468255	0.86[ASN][1000 genomes]
rs34746401	0.81[ASN][1000 genomes]
rs34834687	0.81[ASN][1000 genomes]
rs34849715	0.87[ASN][1000 genomes]
rs35169866	0.84[ASN][1000 genomes]
rs35563598	0.81[ASN][1000 genomes]
rs35761622	0.83[ASN][1000 genomes]
rs3732420	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs71325376	0.86[ASN][1000 genomes]
rs71325378	0.84[ASN][1000 genomes]
rs71618009	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv3962	chr3:119094646-119135321	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1000199	GOLGB1	cis	cerebellum	SCAN
rs1000199	IGSF11	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119072000-119133800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:119072200-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
4	chr3:119081200-119135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:119081400-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:119082800-119138000	Weak transcription	Small Intestine	intestine
7	chr3:119085200-119139000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:119088000-119134200	Weak transcription	NHDF-Ad	bronchial
9	chr3:119088200-119122400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:119093000-119116200	Weak transcription	Psoas Muscle	Psoas
11	chr3:119094400-119119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:119097000-119132600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:119097600-119120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:119098000-119136800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:119098400-119138200	Strong transcription	Adipose Nuclei	Adipose
16	chr3:119098600-119137400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:119099000-119126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:119099200-119120600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:119099600-119124800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:119099800-119114200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:119099800-119114200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:119100000-119115400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:119100000-119118200	Weak transcription	Fetal Heart	heart
24	chr3:119100000-119132600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:119100200-119114600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:119102600-119133200	Weak transcription	NHLF	lung
27	chr3:119102600-119134800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:119103800-119118200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:119105400-119130000	Weak transcription	Fetal Brain Male	brain
30	chr3:119106400-119131200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:119106800-119137400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:119107000-119114600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:119107200-119123000	Strong transcription	HUVEC	blood vessel
34	chr3:119107600-119115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:119108400-119114600	Strong transcription	Left Ventricle	heart
36	chr3:119108400-119125600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:119108800-119114800	Strong transcription	Right Ventricle	heart
38	chr3:119108800-119122800	Strong transcription	NH-A	brain
39	chr3:119109000-119118200	Strong transcription	Placenta	Placenta
40	chr3:119109200-119114200	Strong transcription	Fetal Lung	lung
41	chr3:119109200-119114800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:119109200-119136400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:119109400-119120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:119109400-119130800	Strong transcription	Osteobl	bone
45	chr3:119110200-119115800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:119110200-119120400	Weak transcription	Pancreas	Pancrea
47	chr3:119110200-119128800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:119110200-119140800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:119110400-119132200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:119110800-119118000	Weak transcription	Esophagus	oesophagus

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