Variant report

Variant	rs2642956
Chromosome Location	chr1:247166743-247166744
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10802457	0.80[MEX][hapmap]
rs10802462	1.00[CHD][hapmap]
rs10924888	1.00[ASN][1000 genomes]
rs10924895	0.80[EUR][1000 genomes]
rs10924897	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10924899	1.00[CHD][hapmap]
rs1112137	0.81[EUR][1000 genomes]
rs12060791	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12116484	1.00[CHD][hapmap]
rs12122290	0.81[EUR][1000 genomes]
rs12130075	0.81[EUR][1000 genomes]
rs12135374	1.00[CHD][hapmap]
rs12141355	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs12144260	0.80[EUR][1000 genomes]
rs12563431	1.00[ASN][1000 genomes]
rs12727420	1.00[ASN][1000 genomes]
rs1546143	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1565897	0.85[EUR][1000 genomes]
rs1573897	0.92[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1874200	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2379189	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2380113	0.83[EUR][1000 genomes]
rs2453405	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2453407	0.89[MEX][hapmap]
rs2642957	1.00[ASN][1000 genomes]
rs2642974	1.00[ASN][1000 genomes]
rs2642978	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2642992	0.81[EUR][1000 genomes]
rs2642995	0.83[MEX][hapmap]
rs2818872	1.00[ASN][1000 genomes]
rs2818874	1.00[ASN][1000 genomes]
rs2818893	1.00[ASN][1000 genomes]
rs4319379	0.92[CEU][hapmap]
rs4634944	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4925540	0.92[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4925622	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4925700	1.00[CHD][hapmap]
rs4971315	0.82[EUR][1000 genomes]
rs4971316	0.82[EUR][1000 genomes]
rs4971317	0.82[EUR][1000 genomes]
rs4971319	0.82[EUR][1000 genomes]
rs4971320	1.00[ASN][1000 genomes]
rs4971321	1.00[ASN][1000 genomes]
rs4971322	1.00[ASN][1000 genomes]
rs55984722	0.81[EUR][1000 genomes]
rs56884994	0.82[EUR][1000 genomes]
rs61498462	0.82[EUR][1000 genomes]
rs61852630	0.82[EUR][1000 genomes]
rs61852631	0.81[EUR][1000 genomes]
rs61852637	0.81[EUR][1000 genomes]
rs6426215	0.92[CEU][hapmap]
rs6426216	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6657686	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6664217	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6689229	0.92[CEU][hapmap]
rs6698318	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6698643	1.00[CHD][hapmap]
rs6701582	0.82[EUR][1000 genomes]
rs72768397	0.81[EUR][1000 genomes]
rs7418825	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7511962	0.82[EUR][1000 genomes]
rs7512099	0.83[EUR][1000 genomes]
rs7512150	0.82[EUR][1000 genomes]
rs7513728	0.85[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7519795	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7522300	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7542852	0.92[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7544897	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7546342	0.82[EUR][1000 genomes]
rs7546777	0.82[EUR][1000 genomes]
rs7547915	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs7549105	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs7549410	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv945436	chr1:247162782-247171728	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2642956	OR2AK2	cis	cerebellum	SCAN
rs2642956	OR2L8	cis	parietal	SCAN
rs2642956	ZNF670	cis	cerebellum	SCAN
rs2642956	OR2L8	cis	cerebellum	SCAN
rs2642956	OR2L2	cis	parietal	SCAN
rs2642956	OR2L2	cis	cerebellum	SCAN
rs2642956	ZNF670	cis	parietal	SCAN
rs2642956	SMYD3	cis	parietal	SCAN
rs2642956	OR1C1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247151200-247170800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:247151600-247170000	Weak transcription	Osteobl	bone
3	chr1:247155200-247168800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:247158000-247170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:247158400-247167800	Weak transcription	HUVEC	blood vessel
6	chr1:247159600-247170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:247162800-247168600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:247162800-247168600	Weak transcription	Thymus	Thymus
9	chr1:247163000-247169800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:247163400-247167600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:247163400-247168000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:247163400-247170000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:247163400-247170000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:247163400-247170000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:247163400-247170400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:247163600-247170400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:247164600-247167600	Weak transcription	HepG2	liver
18	chr1:247165600-247169600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:247166000-247169200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr1:247166000-247169200	ZNF genes & repeats	Dnd41	blood
21	chr1:247166200-247166800	ZNF genes & repeats	Hela-S3	cervix
22	chr1:247166400-247168400	ZNF genes & repeats	K562	blood
23	chr1:247166400-247170400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:247166600-247166800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:247166600-247167600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:247166600-247168600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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