Variant report

Variant	rs1548868
Chromosome Location	chr7:78118982-78118983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10156060	0.83[MKK][hapmap];0.86[YRI][hapmap]
rs12670134	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978323	0.86[EUR][1000 genomes]
rs1990577	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2192646	0.87[AFR][1000 genomes]
rs2192647	0.87[AFR][1000 genomes]
rs2362611	0.87[EUR][1000 genomes]
rs35454028	0.87[AFR][1000 genomes]
rs3735442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996259	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs67578259	0.81[AFR][1000 genomes]
rs741254	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741255	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779312	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784896	0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs7785241	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804932	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7807727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975421	0.81[AFR][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
rs1548868	GTF2IRD1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78114800-78127800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:78115000-78119000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:78116600-78125600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:78116800-78119600	Active TSS	Brain Anterior Caudate	brain
5	chr7:78116800-78119600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr7:78117400-78119400	Active TSS	Brain Substantia Nigra	brain
7	chr7:78117600-78119200	Active TSS	Brain Hippocampus Middle	brain
8	chr7:78117600-78119400	Active TSS	Fetal Brain Female	brain
9	chr7:78118200-78119200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:78118200-78119400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:78118200-78119600	Active TSS	Brain Angular Gyrus	brain
12	chr7:78118200-78119600	Active TSS	Ovary	ovary
13	chr7:78118400-78119400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:78118400-78119400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:78118400-78119400	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr7:78118400-78119600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr7:78118400-78119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:78118600-78119000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr7:78118600-78119000	Active TSS	Stomach Smooth Muscle	stomach
20	chr7:78118600-78119200	Enhancers	Fetal Lung	lung
21	chr7:78118600-78119200	Active TSS	Fetal Muscle Leg	muscle
22	chr7:78118600-78119400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr7:78118600-78119400	Enhancers	Colon Smooth Muscle	Colon
24	chr7:78118600-78119400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr7:78118600-78119600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:78118600-78119600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:78118600-78119600	Enhancers	Fetal Heart	heart
28	chr7:78118600-78119800	Active TSS	Brain Cingulate Gyrus	brain
29	chr7:78118600-78123400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr7:78118800-78119000	Enhancers	Fetal Intestine Large	intestine
31	chr7:78118800-78119000	Enhancers	Fetal Intestine Small	intestine
32	chr7:78118800-78119200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:78118800-78119200	Active TSS	Fetal Brain Male	brain
34	chr7:78118800-78119200	Active TSS	Right Atrium	heart
35	chr7:78118800-78119200	Flanking Active TSS	Osteobl	bone
36	chr7:78118800-78119400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr7:78118800-78119400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:78118800-78119400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:78118800-78119400	Active TSS	Aorta	Aorta
40	chr7:78118800-78119400	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr7:78118800-78119400	Active TSS	Fetal Muscle Trunk	muscle
42	chr7:78118800-78119400	Active TSS	NH-A	brain
43	chr7:78118800-78119600	Enhancers	Adipose Nuclei	Adipose
44	chr7:78118800-78119800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr7:78118800-78120200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr7:78118800-78120200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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