Variant report

Variant	rs11572424
Chromosome Location	chr1:217199733-217199734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10863288	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117746	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117747	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117748	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117750	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117751	0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117752	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11117754	0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs11117758	0.93[ASW][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs11572421	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12067977	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12075072	0.97[ASN][1000 genomes]
rs12134950	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142044	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17635993	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17687992	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4113088	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4360582	0.93[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs4846805	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11572424	RD3	cis	cerebellum	SCAN
rs11572424	KCNK2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217194800-217206200	Weak transcription	Left Ventricle	heart
2	chr1:217196000-217206200	Weak transcription	Right Atrium	heart
3	chr1:217196200-217206200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:217197000-217199800	Weak transcription	Fetal Intestine Small	intestine
5	chr1:217197200-217200200	Weak transcription	Fetal Heart	heart
6	chr1:217198200-217200000	Enhancers	Fetal Muscle Leg	muscle
7	chr1:217198600-217200600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:217198600-217200800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:217198600-217203200	Weak transcription	Aorta	Aorta
10	chr1:217199200-217204800	Enhancers	Fetal Kidney	kidney
11	chr1:217199400-217200800	Enhancers	Small Intestine	intestine
12	chr1:217199600-217200000	Weak transcription	Pancreas	Pancrea
13	chr1:217199600-217202400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:217199600-217203800	Enhancers	Fetal Intestine Large	intestine
15	chr1:217199600-217206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:217199600-217211800	Weak transcription	Gastric	stomach

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

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