Variant report

Variant	rs5012181
Chromosome Location	chr4:175376219-175376220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11726385	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11728322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735634	0.96[AFR][1000 genomes]
rs13106936	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs13135838	0.93[AFR][1000 genomes]
rs1426936	0.94[ASN][1000 genomes]
rs17052159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17052161	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17052168	0.88[ASN][1000 genomes]
rs17060554	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs2195039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332896	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332898	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34674779	0.86[AFR][1000 genomes]
rs35223598	0.81[ASN][1000 genomes]
rs35539859	0.86[AFR][1000 genomes]
rs35549890	0.88[ASN][1000 genomes]
rs35706347	0.86[AFR][1000 genomes]
rs35780342	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35906694	0.81[ASN][1000 genomes]
rs35931018	0.86[AFR][1000 genomes]
rs36112171	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147100	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59300323	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62337115	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62337116	0.84[EUR][1000 genomes]
rs62337142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62337143	0.94[ASN][1000 genomes]
rs62337145	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62337147	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62337155	0.88[ASN][1000 genomes]
rs6827776	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666264	0.93[AFR][1000 genomes]
rs7682749	0.88[ASN][1000 genomes]
rs9312555	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	esv3361753	chr4:175375852-175377950	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5012181	HPGD	cis	multi-tissue	Pritchard
rs5012181	SPCS3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175371000-175378400	Weak transcription	Esophagus	oesophagus
2	chr4:175371800-175382600	Weak transcription	Small Intestine	intestine
3	chr4:175372000-175377200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:175374000-175377800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:175374200-175378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:175374400-175377800	Weak transcription	Stomach Mucosa	stomach
7	chr4:175374600-175382800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:175374800-175377000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:175375200-175377000	Weak transcription	Fetal Stomach	stomach
10	chr4:175375800-175376400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr4:175376000-175376600	Enhancers	Fetal Intestine Small	intestine
12	chr4:175376000-175379400	Enhancers	Colon Smooth Muscle	Colon
13	chr4:175376200-175378800	Weak transcription	Pancreas	Pancrea

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