Variant report

Variant	rs6696968
Chromosome Location	chr1:77809846-77809847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:77803574..77805696-chr1:77808373..77811184,2	K562	blood:
2	chr1:77808952..77811153-chr1:77811889..77814837,3	K562	blood:
3	chr1:77800850..77802906-chr1:77808839..77811441,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10873930	0.81[ASN][1000 genomes]
rs11162323	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1616948	0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1670616	0.82[ASN][1000 genomes]
rs1721166	0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1823840	0.81[ASN][1000 genomes]
rs1869467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167994	0.81[ASN][1000 genomes]
rs4949789	0.88[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6696968	LRRIQ3	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77788800-77813000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:77789000-77813000	Weak transcription	NHLF	lung
3	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:77800400-77812800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:77800800-77813400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:77801000-77825800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:77803600-77813400	Weak transcription	Brain Angular Gyrus	brain
10	chr1:77804200-77812400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:77806200-77811000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:77806200-77812800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:77807000-77813000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:77807600-77813000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:77808800-77812800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:77808800-77813600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:77809000-77812800	Strong transcription	NHDF-Ad	bronchial
18	chr1:77809000-77819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:77809200-77812000	Strong transcription	HSMM	muscle
20	chr1:77809200-77813000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:77809200-77814400	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:77809400-77811000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:77809400-77812600	Weak transcription	A549	lung
24	chr1:77809400-77812800	Weak transcription	Primary T cells from cord blood	blood
25	chr1:77809600-77811600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:77809800-77811600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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