Variant report

Variant	rs13410783
Chromosome Location	chr2:36789166-36789167
allele	A/G
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	POLR2A	chr2:36788413-36789352	U87	brain:	n/a	n/a
2	BRCA1	chr2:36788634-36789703	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr2:36788431-36789808	A549	lung:	n/a	n/a
4	FOSL2	chr2:36788364-36789835	SK-N-SH	brain:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
5	POLR2A	chr2:36787825-36789305	A549	lung:	n/a	n/a
6	POLR2A	chr2:36787707-36789341	HUVEC	blood vessel:	n/a	n/a
7	TEAD4	chr2:36788578-36789176	HCT-116	colon:	n/a	n/a
8	FOSL2	chr2:36788294-36789824	A549	lung:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
9	RXRA	chr2:36788470-36789195	SK-N-SH	brain:	n/a	chr2:36788845-36788854
10	TCF12	chr2:36788266-36789815	SK-N-SH	brain:	n/a	chr2:36788912-36788920 chr2:36788940-36788949
11	TCF12	chr2:36788584-36789166	A549	lung:	n/a	chr2:36788912-36788920 chr2:36788940-36788949
12	POLR2A	chr2:36788582-36789293	U87	brain:	n/a	n/a
13	POLR2A	chr2:36786222-36789376	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr2:36788482-36789175	PANC-1	pancreas:	n/a	n/a
15	TEAD4	chr2:36788425-36789217	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:36787894-36789166	HUVEC	blood vessel:	n/a	n/a
17	FOS	chr2:36788164-36789702	HUVEC	blood vessel:	n/a	chr2:36788887-36788898 chr2:36788843-36788854 chr2:36788889-36788897 chr2:36788875-36788884
18	FOS	chr2:36788651-36789703	MCF10A-Er-Src	breast:	n/a	chr2:36788887-36788898 chr2:36788843-36788854 chr2:36788889-36788897 chr2:36788875-36788884
19	EP300	chr2:36788353-36789352	A549	lung:	n/a	chr2:36788872-36788886 chr2:36788873-36788882
20	MAX	chr2:36788331-36789167	HCT-116	colon:	n/a	n/a
21	SP1	chr2:36788413-36789279	HCT-116	colon:	n/a	n/a
22	JUND	chr2:36788454-36789772	Hela-S3	cervix:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
23	JUND	chr2:36788432-36789227	HCT-116	colon:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
24	GATA3	chr2:36787852-36789857	A549	lung:	n/a	chr2:36788874-36788884
25	NFIC	chr2:36788376-36789319	SK-N-SH	brain:	n/a	n/a
26	JUND	chr2:36788390-36789225	HCT-116	colon:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
27	FOSL1	chr2:36788459-36789188	HCT-116	colon:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
28	MAX	chr2:36788282-36789192	A549	lung:	n/a	n/a
29	GATA2	chr2:36788455-36789281	HUVEC	blood vessel:	n/a	chr2:36788874-36788884
30	EP300	chr2:36787862-36789272	A549	lung:	n/a	chr2:36788872-36788886 chr2:36788873-36788882
31	MAX	chr2:36788262-36789279	A549	lung:	n/a	n/a
32	POLR2A	chr2:36788551-36789275	SK-N-SH	brain:	n/a	n/a
33	EP300	chr2:36788357-36789379	SK-N-SH	brain:	n/a	chr2:36788872-36788886 chr2:36788873-36788882
34	EP300	chr2:36788458-36789759	Hela-S3	cervix:	n/a	chr2:36788872-36788886 chr2:36788873-36788882
35	EP300	chr2:36788483-36789181	ECC-1	luminal epithelium:	n/a	chr2:36788872-36788886 chr2:36788873-36788882
36	SMARCC1	chr2:36788466-36789648	Hela-S3	cervix:	n/a	chr2:36788889-36788898
37	POLR2A	chr2:36788413-36789726	U87	brain:	n/a	n/a
38	GATA3	chr2:36788326-36790151	SK-N-SH	brain:	n/a	chr2:36788874-36788884 chr2:36790043-36790056
39	GABPA	chr2:36788612-36789174	A549	lung:	n/a	n/a
40	GATA3	chr2:36788349-36790622	SK-N-SH	brain:	n/a	chr2:36788874-36788884 chr2:36790043-36790056
41	FOSL1	chr2:36788301-36789818	HCT-116	colon:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
42	CEBPB	chr2:36788517-36789200	A549	lung:	n/a	n/a
43	TEAD4	chr2:36788530-36789167	ECC-1	luminal epithelium:	n/a	n/a
44	JUND	chr2:36788307-36789827	SK-N-SH	brain:	n/a	chr2:36788889-36788897 chr2:36788875-36788884
45	PBX3	chr2:36788444-36789208	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr2:36788629-36789293	U87	brain:	n/a	n/a
47	SP1	chr2:36788352-36789895	A549	lung:	n/a	n/a
48	POLR2A	chr2:36787857-36789778	HUVEC	blood vessel:	n/a	n/a
49	REST	chr2:36788432-36789392	A549	lung:	n/a	n/a
50	SP1	chr2:36788332-36789289	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36788852..36791258-chr2:36824096..36825627,2	K562	blood:
2	chr2:36781920..36784587-chr2:36788838..36790616,3	K562	blood:

Variant related genes	Relation type
FEZ2	TF binding region
ENSG00000171055	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10175266	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10178965	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10180760	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10181664	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10189344	0.86[EUR][1000 genomes]
rs10189554	0.91[EUR][1000 genomes]
rs10194100	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10197570	0.86[EUR][1000 genomes]
rs10210291	0.87[EUR][1000 genomes]
rs1045543	0.83[EUR][1000 genomes]
rs10469897	0.88[EUR][1000 genomes]
rs10469898	0.88[EUR][1000 genomes]
rs11124519	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11686443	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11691600	0.89[EUR][1000 genomes]
rs11693359	0.93[EUR][1000 genomes]
rs12105545	0.90[EUR][1000 genomes]
rs12712508	0.82[EUR][1000 genomes]
rs13029475	0.89[EUR][1000 genomes]
rs13385408	0.88[EUR][1000 genomes]
rs13398345	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13406169	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13406184	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14291	0.84[EUR][1000 genomes]
rs1523786	0.91[EUR][1000 genomes]
rs1533946	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533947	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1533948	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533949	0.95[EUR][1000 genomes]
rs17019087	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17488036	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2022211	0.91[EUR][1000 genomes]
rs2072533	0.90[EUR][1000 genomes]
rs2072534	0.90[EUR][1000 genomes]
rs2072535	0.89[EUR][1000 genomes]
rs2075226	0.91[EUR][1000 genomes]
rs2110986	0.91[EUR][1000 genomes]
rs2110987	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160403	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160404	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34392255	0.89[EUR][1000 genomes]
rs34425257	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3755196	0.85[EUR][1000 genomes]
rs3770788	0.89[EUR][1000 genomes]
rs3770797	0.92[EUR][1000 genomes]
rs3770799	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770809	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3770811	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55700228	0.88[EUR][1000 genomes]
rs57670037	0.82[EUR][1000 genomes]
rs6728602	0.90[EUR][1000 genomes]
rs848610	0.85[EUR][1000 genomes]
rs848611	0.84[EUR][1000 genomes]
rs848612	0.82[EUR][1000 genomes]
rs848613	0.84[EUR][1000 genomes]
rs848614	0.82[EUR][1000 genomes]
rs848616	0.84[EUR][1000 genomes]
rs848619	0.84[EUR][1000 genomes]
rs848624	0.85[EUR][1000 genomes]
rs848627	0.81[EUR][1000 genomes]
rs848629	0.86[EUR][1000 genomes]
rs848630	0.86[EUR][1000 genomes]
rs848631	0.87[EUR][1000 genomes]
rs848635	0.88[EUR][1000 genomes]
rs848636	0.87[EUR][1000 genomes]
rs848638	0.89[EUR][1000 genomes]
rs848639	0.88[EUR][1000 genomes]
rs848640	0.85[EUR][1000 genomes]
rs9917316	0.91[EUR][1000 genomes]
rs9917318	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13410783	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
3	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:36764000-36790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:36764800-36791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:36766000-36791800	Weak transcription	Esophagus	oesophagus
7	chr2:36769800-36790400	Weak transcription	Spleen	Spleen
8	chr2:36771400-36802800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:36776600-36792600	Weak transcription	Right Ventricle	heart
11	chr2:36776600-36804800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:36776600-36804800	Weak transcription	Fetal Brain Female	brain
13	chr2:36777400-36790600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:36777400-36795000	Weak transcription	Fetal Heart	heart
15	chr2:36778600-36790400	Weak transcription	Psoas Muscle	Psoas
16	chr2:36779200-36791600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:36779400-36789600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:36779400-36789600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:36779400-36805000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:36779800-36789200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:36780000-36804800	Weak transcription	Brain Germinal Matrix	brain
22	chr2:36780800-36790400	Weak transcription	Pancreas	Pancrea
23	chr2:36781400-36791800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:36782000-36790200	Weak transcription	Thymus	Thymus
25	chr2:36782000-36792400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:36782000-36805400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:36782200-36790400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:36782600-36790400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:36782600-36798400	Weak transcription	Gastric	stomach
30	chr2:36782800-36789600	Weak transcription	Liver	Liver
31	chr2:36782800-36789600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:36782800-36790400	Weak transcription	Fetal Stomach	stomach
33	chr2:36782800-36791800	Weak transcription	Colonic Mucosa	Colon
34	chr2:36782800-36799600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:36783000-36800600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:36783200-36805000	Weak transcription	K562	blood
37	chr2:36783400-36805000	Weak transcription	GM12878-XiMat	blood
38	chr2:36783600-36790400	Weak transcription	Lung	lung
39	chr2:36783600-36792600	Weak transcription	Dnd41	blood
40	chr2:36783800-36794200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:36784800-36799200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:36785200-36800600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:36786400-36789400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:36786400-36789400	Strong transcription	Fetal Intestine Large	intestine
45	chr2:36786400-36792200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:36786400-36794200	Strong transcription	Primary T cells from cord blood	blood
47	chr2:36786400-36794800	Strong transcription	Primary B cells from cord blood	blood
48	chr2:36786600-36790800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:36786600-36792000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:36786600-36793200	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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