Variant report

Variant	rs1111250
Chromosome Location	chr2:179124196-179124197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11902232	0.81[ASN][1000 genomes]
rs12693156	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387048	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]
rs13425013	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17592042	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs334005	0.80[YRI][hapmap]
rs334007	0.83[YRI][hapmap]
rs334042	0.80[YRI][hapmap]
rs34780417	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34835220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433715	0.93[MEX][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs6729314	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741744	1.00[ASN][1000 genomes]
rs6746200	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564722	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]
rs919682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs1111250	C7orf23	trans	parietal	SCAN
rs1111250	SP9	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179111200-179137400	Weak transcription	Right Atrium	heart
2	chr2:179121600-179126400	Weak transcription	K562	blood
3	chr2:179121800-179128000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:179123000-179124800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:179123400-179124200	Enhancers	HMEC	breast
6	chr2:179123600-179124200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:179123600-179124200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:179123600-179124200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr2:179123600-179124200	Enhancers	NHEK	skin
10	chr2:179123600-179124400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:179123800-179124200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:179123800-179125000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:179124000-179124200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:179124000-179130800	Weak transcription	Psoas Muscle	Psoas

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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