Variant report

Variant	rs1434080
Chromosome Location	chr2:179156878-179156879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179141793..179143622-chr2:179155876..179157872,2	K562	blood:
2	chr2:179150083..179151979-chr2:179155800..179158067,3	K562	blood:
3	chr2:179156403..179158773-chr2:179276903..179278454,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10203420	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11680778	0.82[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11692144	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12469658	0.84[EUR][1000 genomes]
rs12473780	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12476671	0.80[EUR][1000 genomes]
rs12693158	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12693160	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13024959	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13382421	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13400738	0.82[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13407992	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1865325	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333992	0.83[JPT][hapmap]
rs333993	0.83[JPT][hapmap]
rs333995	0.82[JPT][hapmap]
rs334604	0.83[JPT][hapmap]
rs334616	0.88[JPT][hapmap]
rs334620	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs334622	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs334623	1.00[JPT][hapmap]
rs334630	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6716156	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6756651	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7587549	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599683	0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9288016	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9288017	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9989738	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1434080	CHN1	cis	parietal	SCAN
rs1434080	LOC100130691	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179143000-179160200	Weak transcription	Fetal Kidney	kidney
2	chr2:179143200-179160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:179144200-179163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:179145000-179159200	Weak transcription	Liver	Liver
6	chr2:179147400-179162600	Weak transcription	HMEC	breast
7	chr2:179147400-179163000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:179147400-179163000	Weak transcription	NHEK	skin
9	chr2:179147800-179162800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:179150200-179160800	Weak transcription	Psoas Muscle	Psoas
11	chr2:179150600-179160600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:179151600-179160800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:179151600-179161200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:179153200-179157200	Weak transcription	K562	blood
15	chr2:179153200-179157400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:179153200-179160200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:179153200-179160200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:179153200-179162800	Weak transcription	HUVEC	blood vessel
19	chr2:179154800-179163000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:179155600-179162600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:179155600-179174200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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