Variant report

Variant	rs6744284
Chromosome Location	chr2:234625297-234625298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10168416	0.85[CEU][hapmap]
rs10173355	0.85[CEU][hapmap]
rs10178992	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10202865	0.85[CEU][hapmap]
rs10929302	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1105879	0.83[GIH][hapmap]
rs1105880	0.83[GIH][hapmap]
rs11673726	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11695484	0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11888459	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11891311	0.82[ASW][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13009407	0.90[CEU][hapmap]
rs13401281	0.91[ASN][1000 genomes]
rs13410335	0.81[ASN][1000 genomes]
rs17862875	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17863787	0.90[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs17864701	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1875263	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1983023	0.88[ASN][1000 genomes]
rs2018985	0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2070959	0.90[CEU][hapmap]
rs2885296	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28899170	0.85[CEU][hapmap]
rs34352510	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3771341	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3806592	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4148324	0.86[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs4148325	0.86[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs4341922	0.85[ASN][1000 genomes]
rs4477910	0.87[ASN][1000 genomes]
rs6714634	0.95[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6722076	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725478	0.81[CHD][hapmap];0.89[GIH][hapmap]
rs6742078	0.86[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs6747843	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6749496	1.00[ASN][1000 genomes]
rs7564935	0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7567229	0.81[EUR][1000 genomes]
rs7567468	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7583278	0.89[GIH][hapmap];0.88[YRI][hapmap]
rs7604115	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs869283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs887829	0.86[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs929596	0.90[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv963781	chr2:234618109-234626863	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv876017	chr2:234618243-234626972	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv3382515	chr2:234620643-234626555	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv3448604	chr2:234622257-234628221	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3460836	chr2:234623884-234634466	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv3460837	chr2:234624010-234634422	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6744284	EFHD1	cis	cerebellum	SCAN
rs6744284	NPPC	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234617800-234631600	Weak transcription	Gastric	stomach
2	chr2:234620400-234659200	Weak transcription	Colonic Mucosa	Colon
3	chr2:234620600-234652200	Weak transcription	Esophagus	oesophagus
4	chr2:234621400-234625800	Weak transcription	Liver	Liver
5	chr2:234621800-234626200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:234622200-234625400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:234622200-234625600	Weak transcription	NHEK	skin
8	chr2:234622200-234627400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:234625000-234626400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:234625200-234626000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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