Variant report

Variant	rs1616948
Chromosome Location	chr1:77768016-77768017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77766400..77769347-chr1:77774174..77776470,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10873930	0.98[ASN][1000 genomes]
rs11162323	0.84[CHB][hapmap];0.95[CHD][hapmap]
rs1167198	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap]
rs1167205	0.90[ASW][hapmap]
rs1670611	0.83[YRI][hapmap]
rs1670612	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs1670616	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1670617	0.90[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs1670618	0.83[YRI][hapmap]
rs1721165	0.90[ASW][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs1721166	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779178	0.84[YRI][hapmap]
rs1823840	0.98[ASN][1000 genomes]
rs1869467	0.83[ASN][1000 genomes]
rs2167994	0.98[ASN][1000 genomes]
rs2602953	0.90[ASW][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs2815313	0.90[ASW][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs4949789	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4949790	0.90[ASN][1000 genomes]
rs6696968	0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.82[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1616948	LRRIQ3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77749000-77779200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77749200-77778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77749400-77781600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:77749800-77768800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:77750600-77772400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:77750800-77768200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:77754400-77785800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:77755000-77768800	Strong transcription	NHDF-Ad	bronchial
9	chr1:77755200-77781600	Weak transcription	Osteobl	bone
10	chr1:77755800-77788200	Weak transcription	HSMMtube	muscle
11	chr1:77756800-77781600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:77757600-77777400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:77758000-77778400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:77758600-77771000	Weak transcription	Brain Anterior Caudate	brain
15	chr1:77759000-77781600	Weak transcription	NHLF	lung
16	chr1:77763600-77769200	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:77766000-77768800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:77767200-77768800	Weak transcription	Primary T cells from cord blood	blood
19	chr1:77767200-77773600	Weak transcription	HSMM	muscle
20	chr1:77767400-77769400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:77767400-77773400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:77767400-77774200	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:77767600-77774400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:77767600-77776600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:77767800-77773400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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