Variant report

Variant	rs13387048
Chromosome Location	chr2:179109539-179109540
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	chr2:179109388..179113202-chr2:179114202..179117168,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1111250	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11902232	0.94[ASN][1000 genomes]
rs12693156	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17592042	0.89[CEU][hapmap]
rs34780417	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34835220	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35313685	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433715	0.86[CHB][hapmap];0.96[CHD][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs6729314	0.90[EUR][1000 genomes]
rs6741744	0.88[ASN][1000 genomes]
rs6746200	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7564722	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]
rs919682	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.88[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
rs13387048	C7orf23	trans	parietal	SCAN
rs13387048	SP9	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179091200-179115000	Weak transcription	Aorta	Aorta
2	chr2:179101000-179115400	Weak transcription	Gastric	stomach
3	chr2:179104200-179111000	Weak transcription	Left Ventricle	heart
4	chr2:179105400-179120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179106600-179115200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:179106800-179115200	Weak transcription	Pancreas	Pancrea
7	chr2:179107200-179109600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:179107200-179110200	Weak transcription	HSMMtube	muscle
9	chr2:179107200-179110400	Weak transcription	Right Atrium	heart
10	chr2:179107200-179112400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:179107200-179115400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:179107200-179116000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:179107400-179109600	Weak transcription	K562	blood
14	chr2:179107400-179109800	Weak transcription	HMEC	breast
15	chr2:179107400-179112000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:179107400-179112000	Weak transcription	HSMM	muscle
17	chr2:179107400-179112400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:179107400-179115200	Weak transcription	Fetal Lung	lung
19	chr2:179107600-179111000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:179107600-179115000	Weak transcription	Fetal Brain Female	brain
21	chr2:179107600-179115400	Weak transcription	Brain Anterior Caudate	brain
22	chr2:179107800-179123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:179108000-179111600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:179108200-179112200	Weak transcription	Right Ventricle	heart
25	chr2:179108400-179115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:179108400-179115800	Weak transcription	Fetal Brain Male	brain
27	chr2:179109000-179109800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:179109000-179109800	Weak transcription	Psoas Muscle	Psoas
29	chr2:179109200-179109800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:179109200-179111000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:179109400-179110600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr2:179109400-179115200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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