Variant report

Variant	rs1345529
Chromosome Location	chr1:197433329-197433330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10801607	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10922231	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10922236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10922260	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1135810	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs12026564	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042609	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1337166	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1923759	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs2111930	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2494268	0.81[YRI][hapmap]
rs2821102	0.84[YRI][hapmap]
rs4026514	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs4147323	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs4274099	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4418639	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4604725	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs61829439	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534863	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs927510	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs9787082	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1345529	LHX2	trans	parietal	SCAN
rs1345529	DENND1B	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197430800-197439000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:197431600-197433600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:197431800-197433600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:197431800-197435400	Enhancers	Brain Germinal Matrix	brain
5	chr1:197432000-197433600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:197432000-197433600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:197432000-197433600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:197432000-197433800	Enhancers	Fetal Intestine Large	intestine
9	chr1:197432000-197434200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:197432000-197436200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:197432200-197433600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:197432200-197434200	Enhancers	Fetal Brain Female	brain
13	chr1:197432200-197439600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:197432400-197433400	Enhancers	Liver	Liver
15	chr1:197432400-197433600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:197432400-197433800	Enhancers	Fetal Lung	lung
17	chr1:197432400-197433800	Enhancers	NH-A	brain
18	chr1:197432400-197435200	Weak transcription	Ovary	ovary
19	chr1:197432600-197433600	Enhancers	Fetal Stomach	stomach
20	chr1:197432600-197434000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:197432800-197439000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:197433000-197433400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:197433000-197433400	Enhancers	Adipose Nuclei	Adipose
24	chr1:197433000-197433600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:197433000-197433600	Enhancers	Fetal Kidney	kidney
26	chr1:197433000-197433800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:197433000-197433800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:197433000-197434000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:197433000-197439000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:197433200-197433400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:197433200-197433400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:197433200-197433400	Enhancers	Right Atrium	heart
33	chr1:197433200-197433400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:197433200-197433400	Enhancers	Osteobl	bone
35	chr1:197433200-197433600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:197433200-197433600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:197433200-197433600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr1:197433200-197433600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:197433200-197433600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:197433200-197433600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:197433200-197433600	Enhancers	Aorta	Aorta
42	chr1:197433200-197433600	Flanking Active TSS	Fetal Brain Male	brain
43	chr1:197433200-197439000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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