Variant report

Variant	rs34777730
Chromosome Location	chr2:64250804-64250805
allele	C/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	MAFK	chr2:64250652-64252223	HepG2	liver:	n/a	n/a
2	MAFF	chr2:64250732-64250956	K562	blood:	n/a	chr2:64250863-64250881
3	TEAD4	chr2:64250647-64252260	HepG2	liver:	n/a	n/a
4	MBD4	chr2:64250639-64252219	HepG2	liver:	n/a	n/a
5	NFIC	chr2:64250766-64252153	HepG2	liver:	n/a	n/a
6	FOXA2	chr2:64250688-64252371	HepG2	liver:	n/a	chr2:64251798-64251810
7	HDAC2	chr2:64250782-64252202	HepG2	liver:	n/a	n/a
8	FOXA1	chr2:64250722-64252220	HepG2	liver:	n/a	chr2:64251798-64251810
9	NFIC	chr2:64250665-64252279	HepG2	liver:	n/a	n/a
10	MAFK	chr2:64250675-64252199	HepG2	liver:	n/a	n/a
11	JUND	chr2:64250754-64251116	HepG2	liver:	n/a	n/a
12	MAFK	chr2:64250672-64250993	IMR90	lung:	n/a	n/a
13	FOXA1	chr2:64250781-64252173	HepG2	liver:	n/a	chr2:64251798-64251810
14	MYBL2	chr2:64250714-64252325	HepG2	liver:	n/a	n/a
15	MAFF	chr2:64250658-64252170	HepG2	liver:	n/a	chr2:64250863-64250881
16	RAD21	chr2:64250776-64251297	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64244419..64248447-chr2:64249482..64256147,6	MCF-7	breast:

Variant related genes	Relation type
VPS54	TF binding region
ENSG00000143952	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10183479	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10865344	0.91[YRI][hapmap]
rs11558741	0.88[ASN][1000 genomes]
rs11674020	0.90[ASN][1000 genomes]
rs11676710	1.00[ASN][1000 genomes]
rs11683408	0.96[ASN][1000 genomes]
rs11691987	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs12713498	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12996866	0.88[ASN][1000 genomes]
rs13018690	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13431781	0.88[ASN][1000 genomes]
rs1440002	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17562177	0.90[ASN][1000 genomes]
rs17562423	0.98[ASN][1000 genomes]
rs193031	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2302808	0.90[ASN][1000 genomes]
rs2439183	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2969395	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329478	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329488	0.91[ASN][1000 genomes]
rs329502	0.85[CHB][hapmap]
rs34122334	0.92[ASN][1000 genomes]
rs34765999	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002211	0.90[ASN][1000 genomes]
rs35336851	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35480874	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35697586	1.00[ASN][1000 genomes]
rs35960986	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36033991	0.90[ASN][1000 genomes]
rs36123537	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233930	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4538187	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs4671071	0.83[ASN][1000 genomes]
rs4671073	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs56904032	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546029	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6546030	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6546032	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6546033	0.87[ASN][1000 genomes]
rs6546035	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs66980330	0.88[ASN][1000 genomes]
rs6710763	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	0.91[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs67308158	0.88[ASN][1000 genomes]
rs6731508	0.88[ASN][1000 genomes]
rs6732746	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs6755646	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs67615384	0.92[ASN][1000 genomes]
rs67765474	0.90[ASN][1000 genomes]
rs68117986	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808243	0.88[ASN][1000 genomes]
rs72893103	0.96[ASN][1000 genomes]
rs74181291	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7590399	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34777730	UGP2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64247200-64251000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:64247200-64251000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:64247200-64251000	Weak transcription	Fetal Thymus	thymus
4	chr2:64247200-64251000	Weak transcription	Pancreas	Pancrea
5	chr2:64247200-64251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:64247200-64254200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:64247400-64253000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:64247400-64253800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:64247600-64251000	Weak transcription	GM12878-XiMat	blood
10	chr2:64247600-64262800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:64248000-64251000	Weak transcription	Thymus	Thymus
12	chr2:64248000-64252600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:64248400-64252600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:64249000-64251200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:64249000-64252400	Weak transcription	Primary T cells from cord blood	blood
16	chr2:64249000-64252600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:64249000-64252600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:64249000-64254000	Weak transcription	K562	blood
19	chr2:64249000-64256200	Weak transcription	NHDF-Ad	bronchial
20	chr2:64249200-64252200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:64249200-64252400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:64249200-64253000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:64249200-64253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:64250600-64251400	Enhancers	Stomach Mucosa	stomach
25	chr2:64250600-64252000	Flanking Active TSS	HepG2	liver
26	chr2:64250600-64252600	Enhancers	Liver	Liver
27	chr2:64250800-64251000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr2:64250800-64251000	Enhancers	HSMMtube	muscle
29	chr2:64250800-64251200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:64250800-64251200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:64250800-64251200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:64250800-64251200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:64250800-64251200	Enhancers	Small Intestine	intestine
34	chr2:64250800-64251200	Enhancers	A549	lung
35	chr2:64250800-64251400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr2:64250800-64251400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:64250800-64251400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr2:64250800-64251400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr2:64250800-64251400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr2:64250800-64251400	Enhancers	Dnd41	blood
41	chr2:64250800-64252200	Enhancers	Fetal Intestine Small	intestine
42	chr2:64250800-64252400	Enhancers	Fetal Intestine Large	intestine

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