Variant report

Variant	rs7564722
Chromosome Location	chr2:179121043-179121044
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	chr2:179114503..179117797-chr2:179118067..179122993,4	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1111250	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12693156	0.87[CEU][hapmap];0.92[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13387048	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13425013	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17592042	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs334005	0.80[YRI][hapmap]
rs334007	0.83[YRI][hapmap]
rs334042	0.80[YRI][hapmap]
rs34780417	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34835220	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35313685	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433715	0.85[MEX][hapmap];0.82[YRI][hapmap]
rs6729314	0.90[EUR][1000 genomes]
rs6741744	0.89[ASN][1000 genomes]
rs6746200	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs919682	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7564722	SP9	cis	parietal	SCAN
rs7564722	C7orf23	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179107800-179123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:179111200-179137400	Weak transcription	Right Atrium	heart
3	chr2:179119400-179121200	Enhancers	Brain Anterior Caudate	brain
4	chr2:179120200-179121600	Enhancers	Fetal Muscle Leg	muscle
5	chr2:179120200-179122000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:179120400-179121800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:179120400-179121800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:179120400-179121800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:179120400-179121800	Enhancers	Brain Angular Gyrus	brain
10	chr2:179120600-179121200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:179120600-179121200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:179120600-179121400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr2:179120600-179121400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:179120600-179121400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:179120600-179121400	Enhancers	Psoas Muscle	Psoas
16	chr2:179120600-179121600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:179120600-179121600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:179120600-179121800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:179120600-179121800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:179120600-179121800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:179120600-179121800	Enhancers	NH-A	brain
22	chr2:179120600-179122000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:179120600-179122000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:179120600-179122000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:179120800-179121400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:179120800-179121600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:179120800-179121600	Enhancers	HSMMtube	muscle
28	chr2:179120800-179121600	Enhancers	K562	blood
29	chr2:179120800-179123800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:179121000-179121400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:179121000-179121400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:179121000-179121800	Enhancers	Fetal Kidney	kidney
33	chr2:179121000-179122000	Enhancers	HSMM	muscle
34	chr2:179121000-179123600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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