Variant report

Variant	rs11887574
Chromosome Location	chr2:100109251-100109252
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:100109225-100109523	HepG2	liver:	n/a	chr2:100109381-100109394
2	CEBPB	chr2:100109241-100109559	IMR90	lung:	n/a	chr2:100109384-100109395
3	CEBPB	chr2:100109204-100109576	HepG2	liver:	n/a	chr2:100109384-100109395
4	JUND	chr2:100109212-100109528	HepG2	liver:	n/a	n/a
5	CEBPB	chr2:100109223-100109563	A549	lung:	n/a	chr2:100109384-100109395
6	CEBPB	chr2:100109211-100109551	K562	blood:	n/a	chr2:100109384-100109395

No.	Distal block	Cell Line	Cell type
1	chr2:100108007..100111568-chr2:100119889..100123182,3	K562	blood:
2	chr2:100105801..100108163-chr2:100108777..100110702,3	K562	blood:
3	chr2:100106008..100108936-chr2:100109053..100113272,5	MCF-7	breast:
4	chr2:100105579..100107417-chr2:100107751..100110835,3	MCF-7	breast:

Variant related genes	Relation type
REV1	TF binding region
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1000409	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1011633	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10170425	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172068	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172752	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10173466	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10186340	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10187843	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10205985	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10207981	0.90[JPT][hapmap]
rs1053544	0.84[JPT][hapmap]
rs11123782	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11123786	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674219	0.81[EUR][1000 genomes]
rs11679115	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11683651	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11686535	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11687870	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11884686	0.84[JPT][hapmap]
rs11887109	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11892441	0.84[JPT][hapmap]
rs11899745	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs11902994	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12464535	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12464785	0.84[JPT][hapmap]
rs12465846	0.80[ASN][1000 genomes]
rs12478488	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12618779	0.82[EUR][1000 genomes]
rs12621141	0.82[AMR][1000 genomes]
rs12623540	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13014360	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs13017871	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13018274	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs13026997	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13028869	0.81[EUR][1000 genomes]
rs13384883	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13389623	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13392042	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13394688	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13427780	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1376443	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1451243	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451246	0.80[ASN][1000 genomes]
rs1584647	0.84[JPT][hapmap]
rs1584648	0.84[JPT][hapmap]
rs17022629	0.84[JPT][hapmap]
rs1807985	0.84[EUR][1000 genomes]
rs1839666	0.83[ASN][1000 genomes]
rs1901283	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973011	0.83[ASN][1000 genomes]
rs2053917	0.80[ASN][1000 genomes]
rs2122748	0.80[ASN][1000 genomes]
rs2242037	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290255	0.84[JPT][hapmap]
rs2290256	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2290257	0.84[JPT][hapmap]
rs2290261	0.84[JPT][hapmap]
rs2305354	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2309585	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309586	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2309604	0.81[ASN][1000 genomes]
rs2309617	0.84[JPT][hapmap]
rs28369943	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28382954	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3087386	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749087	0.84[JPT][hapmap]
rs3791212	0.84[JPT][hapmap]
rs3792134	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792137	0.81[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs3792142	0.83[JPT][hapmap]
rs3792144	0.80[ASN][1000 genomes]
rs3792146	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792149	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792152	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3811555	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3828316	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4143760	0.81[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4476396	0.80[ASN][1000 genomes]
rs4535093	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850901	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4850903	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851200	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs4851205	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851206	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs4851208	0.83[ASN][1000 genomes]
rs60257640	0.80[ASN][1000 genomes]
rs62155809	0.81[ASN][1000 genomes]
rs6542879	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542880	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542882	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6706607	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6708861	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6709240	0.82[EUR][1000 genomes]
rs6713792	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714244	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6715321	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs6717515	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721297	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs6722617	0.90[JPT][hapmap]
rs6734290	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6737560	0.81[ASN][1000 genomes]
rs6761390	0.80[ASN][1000 genomes]
rs717454	0.84[JPT][hapmap]
rs7558074	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7560795	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7561079	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7563455	0.80[ASN][1000 genomes]
rs7563462	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7564587	0.81[ASN][1000 genomes]
rs7567674	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7571202	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7574135	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7579403	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7580448	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585019	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7585721	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7586892	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7587419	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7591212	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7593274	0.84[JPT][hapmap]
rs7594838	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs7597141	0.84[JPT][hapmap]
rs7598629	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7601470	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7601730	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7609108	0.82[EUR][1000 genomes]
rs769105	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs896248	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs896249	0.81[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs959929	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806302	chr2:100094799-100123030	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1809009	chr2:100103752-100109251	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv582524	chr2:100103752-100110353	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11887574	FAHD2A	cis	cerebellum	SCAN
rs11887574	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11887574	LIPT1	cis	multi-tissue	Pritchard
rs11887574	TSGA10	cis	cerebellum	SCAN
rs11887574	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs11887574	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs11887574	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs11887574	TSGA10	cis	multi-tissue	Pritchard
rs11887574	LIPT1	cis	cerebellum	SCAN
rs11887574	LIPT1	cis	parietal	SCAN
rs11887574	REV1L	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100107400-100110400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:100107400-100111600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:100107600-100109600	Weak transcription	Fetal Stomach	stomach
4	chr2:100107600-100110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:100107600-100111600	Weak transcription	Fetal Kidney	kidney
6	chr2:100107600-100111600	Weak transcription	Fetal Lung	lung
7	chr2:100107600-100111800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:100107600-100111800	Weak transcription	A549	lung
9	chr2:100107600-100112400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:100107600-100112400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:100107600-100113000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:100107600-100119600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:100107800-100111600	Weak transcription	K562	blood
14	chr2:100108800-100109400	Enhancers	HepG2	liver
15	chr2:100109200-100109600	Weak transcription	Duodenum Mucosa	Duodenum

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