Variant report

Variant	rs17022433
Chromosome Location	chr2:99873658-99873659
allele	A/T
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	EP300	chr2:99872950-99873679	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
LYG2	TF binding region

Extended variants
information (count: 141 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10172752	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs10187843	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1053544	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs11123775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123777	0.88[ASN][1000 genomes]
rs11123779	0.88[ASN][1000 genomes]
rs11123782	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11123785	0.89[JPT][hapmap]
rs11123786	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11676581	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11683651	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11685870	0.87[ASN][1000 genomes]
rs11686535	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11687328	0.86[ASN][1000 genomes]
rs11687870	0.84[JPT][hapmap]
rs11884686	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11892441	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11892472	0.80[ASN][1000 genomes]
rs11895206	0.82[ASN][1000 genomes]
rs11899745	0.81[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs11902994	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12053519	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12233086	0.89[JPT][hapmap]
rs12233126	0.89[JPT][hapmap]
rs12464785	0.94[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs12475639	0.84[ASN][1000 genomes]
rs12623540	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs13004376	0.85[ASN][1000 genomes]
rs13008948	0.82[ASN][1000 genomes]
rs13009884	0.88[ASN][1000 genomes]
rs13010416	0.88[ASN][1000 genomes]
rs13011240	0.88[ASN][1000 genomes]
rs13014360	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs13016182	0.88[ASN][1000 genomes]
rs13017871	0.84[JPT][hapmap]
rs13018274	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs13019192	0.80[ASN][1000 genomes]
rs13026997	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs13033740	0.88[ASN][1000 genomes]
rs1451243	0.84[JPT][hapmap]
rs1451245	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1584647	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1584648	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs17022564	0.94[ASW][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs17022629	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1825770	0.88[ASN][1000 genomes]
rs1955393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200578	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2242036	0.88[JPT][hapmap]
rs2242037	0.85[CHD][hapmap]
rs2290255	0.94[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs2290256	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2290257	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2290261	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs2305354	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2309585	0.84[JPT][hapmap]
rs2309617	0.94[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs28382892	0.89[JPT][hapmap]
rs3087386	0.84[JPT][hapmap]
rs3749087	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs3791212	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs3792135	0.87[JPT][hapmap]
rs3792136	0.82[JPT][hapmap]
rs3792137	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs3792142	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3792146	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs3792149	0.84[JPT][hapmap]
rs3792152	0.84[CHB][hapmap]
rs3811555	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3828316	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4535093	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4850899	0.88[ASN][1000 genomes]
rs4850901	0.84[JPT][hapmap]
rs4851200	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs4851205	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4851206	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs55815229	0.82[ASN][1000 genomes]
rs55991925	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57242893	0.82[ASN][1000 genomes]
rs58086269	0.81[ASN][1000 genomes]
rs59661148	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59816625	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153855	0.81[ASN][1000 genomes]
rs6542879	0.84[JPT][hapmap]
rs6542880	0.84[JPT][hapmap]
rs6708861	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs6711977	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs6721297	0.81[CHB][hapmap]
rs6722617	0.80[CHB][hapmap]
rs6727483	0.89[JPT][hapmap]
rs6732397	0.87[ASN][1000 genomes]
rs6734290	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs6735381	0.88[ASN][1000 genomes]
rs6753588	0.80[ASN][1000 genomes]
rs717454	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs7421284	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561079	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7561616	0.86[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7563462	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7567674	0.84[JPT][hapmap]
rs7570978	0.87[ASN][1000 genomes]
rs7571202	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7574135	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7579403	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs7580448	0.84[JPT][hapmap]
rs7585721	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7587419	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7593274	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7594838	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs7597141	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7601470	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7601730	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs901596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1001784	chr2:99838079-99910328	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv535840	chr2:99838079-99910328	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv997436	chr2:99840131-99916886	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	esv2762746	chr2:99840143-99916898	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv1001736	chr2:99846306-99916886	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
19	esv2751904	chr2:99847882-99913998	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1001235	chr2:99847890-99913998	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
22	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv1007249	chr2:99855978-99916886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv1004291	chr2:99855978-99919999	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
26	nsv1010419	chr2:99857259-99897312	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
28	esv2842	chr2:99871889-99874318	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17022433	LYG1	cis	multi-tissue	Pritchard
rs17022433	LYG1	cis	Liver	GTEx
rs17022433	LYG1	cis	Adipose Subcutaneous	GTEx
rs17022433	TSGA10	cis	cerebellum	SCAN
rs17022433	LOC129530	cis	multi-tissue	Pritchard
rs17022433	TSGA10	cis	multi-tissue	Pritchard
rs17022433	LYG1	cis	Nerve Tibial	GTEx
rs17022433	LIPT1	cis	cerebellum	SCAN
rs17022433	REV1L	cis	multi-tissue	Pritchard
rs17022433	IL1R2	cis	cerebellum	SCAN
rs17022433	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs17022433	FAHD2B	cis	parietal	SCAN
rs17022433	NM_174898	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99840800-99874400	Weak transcription	Aorta	Aorta
2	chr2:99860400-99899800	Weak transcription	Psoas Muscle	Psoas
3	chr2:99861200-99879200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:99861200-99900800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99861800-99899400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:99862000-99879200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:99869800-99880000	Weak transcription	Right Ventricle	heart
8	chr2:99872000-99873800	Enhancers	HMEC	breast
9	chr2:99873000-99873800	Enhancers	NHEK	skin
10	chr2:99873000-99877600	Weak transcription	Esophagus	oesophagus
11	chr2:99873200-99875600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:99873400-99877600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:99873600-99877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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