Variant report

Variant	rs10485896
Chromosome Location	chr7:78103473-78103474
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	chr7:78099297..78101334-chr7:78102947..78104837,2	K562	blood:
2	chr7:78096180..78099029-chr7:78101096..78103998,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10235821	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10238963	0.88[CEU][hapmap];0.89[GIH][hapmap]
rs10241491	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10251915	0.82[GIH][hapmap]
rs10279188	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10279625	0.80[CEU][hapmap]
rs11763781	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11975402	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12155286	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs12705477	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12705478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12705483	1.00[CEU][hapmap]
rs13237945	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17435216	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs34174742	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71573385	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71573386	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791806	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7794836	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7807844	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10485896	GTF2IRD1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78099600-78104400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:78099800-78106200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:78101800-78105600	Enhancers	Brain Anterior Caudate	brain
4	chr7:78102000-78103600	Enhancers	Brain Hippocampus Middle	brain
5	chr7:78102200-78108200	Weak transcription	Ovary	ovary
6	chr7:78102600-78103800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr7:78102600-78105000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:78102600-78106400	Weak transcription	HSMMtube	muscle
9	chr7:78103000-78103600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:78103000-78103600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:78103000-78103800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:78103000-78117600	Weak transcription	Fetal Brain Female	brain
13	chr7:78103200-78103600	Flanking Active TSS	Fetal Heart	heart
14	chr7:78103200-78103800	Enhancers	Psoas Muscle	Psoas
15	chr7:78103200-78105000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:78103200-78105800	Weak transcription	HSMM	muscle
17	chr7:78103200-78106000	Weak transcription	Brain Substantia Nigra	brain
18	chr7:78103400-78103600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:78103400-78105400	Weak transcription	Osteobl	bone
20	chr7:78103400-78108600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:78103400-78108600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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