Variant report

Variant	rs887829
Chromosome Location	chr2:234668570-234668571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10168416	0.90[CEU][hapmap]
rs10173355	0.90[CEU][hapmap]
rs10178992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10202865	0.90[CEU][hapmap]
rs10929302	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11673726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11695484	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11888459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11891311	0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs13401281	0.87[ASN][1000 genomes]
rs13410335	0.87[ASN][1000 genomes]
rs17862875	0.90[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17863787	0.95[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs17864701	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875263	0.86[JPT][hapmap]
rs1983023	0.90[ASN][1000 genomes]
rs2018985	0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2070959	0.95[CEU][hapmap]
rs2602376	0.81[CEU][hapmap]
rs2741044	0.81[CEU][hapmap]
rs2741045	0.81[CEU][hapmap]
rs2741046	0.81[CEU][hapmap]
rs2885296	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28899170	0.90[CEU][hapmap]
rs34352510	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3771341	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148325	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341922	0.81[ASN][1000 genomes]
rs4477910	0.90[ASN][1000 genomes]
rs6431625	0.82[ASN][1000 genomes]
rs6714634	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6722076	0.95[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6742078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744284	0.86[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs6747843	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564935	0.83[ASW][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.91[ASN][1000 genomes]
rs7567229	0.81[EUR][1000 genomes]
rs7567468	0.91[ASN][1000 genomes]
rs7604115	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs869283	0.86[JPT][hapmap]
rs929596	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv3215	chr2:234631123-234670276	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:8)

Disease	PMID	Source
Bilirubin levels	23642732	GWAS catalog
Metabolite levels	23281178	GWAS catalog
Blood metabolite levels	24816252	GWAS catalog
Bilirubin levels	19419973	GWAS catalog
Cholelithiasis-related traits in sickle cell anemia	22558097	GWAS catalog
Serum metabolite levels	24625756	GWAS catalog
Bilirubin levels	22085899	GWAS catalog
Metabolic traits	21886157	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs887829	EFHD1	cis	cerebellum	SCAN
rs887829	NPPC	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234664000-234669000	Weak transcription	Esophagus	oesophagus
2	chr2:234664000-234669200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:234664200-234668800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:234664200-234669000	Enhancers	Liver	Liver
5	chr2:234664800-234671000	Enhancers	Fetal Intestine Small	intestine
6	chr2:234665200-234669200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:234665600-234670800	Enhancers	Fetal Intestine Large	intestine
8	chr2:234666400-234670200	Bivalent Enhancer	HepG2	liver
9	chr2:234666800-234669200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:234666800-234673600	Weak transcription	Colonic Mucosa	Colon
11	chr2:234667200-234672400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:234667200-234673800	Enhancers	Stomach Mucosa	stomach
13	chr2:234667600-234668800	Weak transcription	A549	lung
14	chr2:234667600-234669000	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:234667600-234670000	Weak transcription	Osteobl	bone
16	chr2:234667800-234668600	Enhancers	Small Intestine	intestine
17	chr2:234667800-234669000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:234667800-234669200	Enhancers	Gastric	stomach
19	chr2:234668200-234669000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:234668400-234669400	Enhancers	NHEK	skin

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