Variant report

Variant	rs763443
Chromosome Location	chr4:90819961-90819962
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	GATA1	chr4:90819108-90820719	PBDE	blood:	n/a	n/a
2	GATA2	chr4:90819403-90820818	HUVEC	blood vessel:	n/a	chr4:90820520-90820534
3	POLR2A	chr4:90818988-90820082	HUVEC	blood vessel:	n/a	n/a
4	BHLHE40	chr4:90819476-90820002	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:90818661-90820935	HUVEC	blood vessel:	n/a	n/a
6	EBF1	chr4:90819524-90819988	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:90818988-90820108	HUVEC	blood vessel:	n/a	n/a
8	MAZ	chr4:90819573-90819964	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90817680..90820518-chr4:90823255..90825762,2	K562	blood:

Variant related genes	Relation type
MMRN1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10001067	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10004413	0.86[EUR][1000 genomes]
rs10005233	0.83[MEX][hapmap]
rs10028246	0.81[EUR][1000 genomes]
rs12331318	0.86[EUR][1000 genomes]
rs1348224	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372507	0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1372517	0.82[AMR][1000 genomes]
rs1372521	0.82[EUR][1000 genomes]
rs1372522	0.82[EUR][1000 genomes]
rs1442129	0.85[CHD][hapmap]
rs1442134	0.93[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1442135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442140	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471483	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs1899389	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011543	0.82[ASN][1000 genomes]
rs2301134	0.88[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2301135	0.81[EUR][1000 genomes]
rs2736994	0.98[ASN][1000 genomes]
rs28403500	0.86[EUR][1000 genomes]
rs28415623	0.81[EUR][1000 genomes]
rs28507349	0.81[EUR][1000 genomes]
rs28734152	0.86[EUR][1000 genomes]
rs28777703	0.86[EUR][1000 genomes]
rs35424815	0.86[EUR][1000 genomes]
rs3756059	0.85[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3756063	0.80[EUR][1000 genomes]
rs3806789	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58864428	0.81[EUR][1000 genomes]
rs6532192	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532193	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6812192	0.93[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6816736	0.82[EUR][1000 genomes]
rs6817001	0.82[EUR][1000 genomes]
rs6828271	0.81[AMR][1000 genomes]
rs6831847	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839608	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843084	0.82[EUR][1000 genomes]
rs6848181	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656954	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671549	0.86[EUR][1000 genomes]
rs7672979	0.86[EUR][1000 genomes]
rs7680557	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7680761	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7681154	0.83[EUR][1000 genomes]
rs7681440	0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs7687945	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7691487	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7698219	0.86[EUR][1000 genomes]
rs894280	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs920624	0.81[AMR][1000 genomes]
rs9307077	0.89[CHD][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs763443	SNORD58A	trans	cerebellum	SCAN
rs763443	MMRN1	cis	cerebellum	SCAN
rs763443	SNCA	cis	cerebellum	SCAN
rs763443	MMRN1	cis	lymphoblastoid	seeQTL
rs763443	MMRN1	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90815800-90820600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:90816400-90822200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:90817400-90820000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:90817400-90823200	Enhancers	Dnd41	blood
5	chr4:90817800-90822200	Enhancers	Primary T cells from cord blood	blood
6	chr4:90818800-90822400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:90818800-90823200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:90819000-90820600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr4:90819200-90820000	Enhancers	Fetal Intestine Large	intestine
10	chr4:90819200-90820000	Enhancers	Fetal Intestine Small	intestine
11	chr4:90819200-90820200	Enhancers	Stomach Mucosa	stomach
12	chr4:90819200-90820400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:90819200-90820600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:90819200-90820800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:90819400-90820000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:90819400-90820400	Enhancers	Primary B cells from cord blood	blood
17	chr4:90819400-90820800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:90819400-90820800	Enhancers	GM12878-XiMat	blood
19	chr4:90819400-90821000	Flanking Active TSS	HUVEC	blood vessel
20	chr4:90819400-90821200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr4:90819600-90820000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:90819600-90820000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr4:90819600-90820000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:90819600-90820000	Enhancers	Fetal Thymus	thymus
25	chr4:90819600-90820000	Enhancers	Small Intestine	intestine
26	chr4:90819600-90820400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:90819600-90820600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:90819600-90821200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:90819800-90820000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:90819800-90820000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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