Variant report

Variant	rs10178965
Chromosome Location	chr2:36782656-36782657
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	chr2:36779682-36783569	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:36782132-36782947	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:36782600-36785091	IMR90	lung:	n/a	n/a
4	POLR2A	chr2:36778965-36784323	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:36778885-36782748	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:36782586-36784761	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:36778760-36784779	SK-N-SH	brain:	n/a	n/a
8	BCL3	chr2:36779978-36784433	A549	lung:	n/a	chr2:36780871-36780880 chr2:36782308-36782317
9	POLR2A	chr2:36780183-36787605	A549	lung:	n/a	n/a
10	POLR2A	chr2:36778741-36783444	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:36782617-36782879	ProgFib	skin:	n/a	n/a
12	POLR2A	chr2:36782645-36782970	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36773463..36777195-chr2:36780018..36782805,3	K562	blood:
2	chr2:36781920..36784587-chr2:36788838..36790616,3	K562	blood:

Variant related genes	Relation type
ENSG00000217075	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10172196	0.80[EUR][1000 genomes]
rs10175266	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10180760	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10181664	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10189344	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10189554	0.91[EUR][1000 genomes]
rs10194100	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10197570	0.86[EUR][1000 genomes]
rs10210291	0.88[EUR][1000 genomes]
rs1045543	0.84[EUR][1000 genomes]
rs10469897	0.89[EUR][1000 genomes]
rs10469898	0.89[EUR][1000 genomes]
rs11124519	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11686443	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11691600	0.90[EUR][1000 genomes]
rs11693359	0.93[EUR][1000 genomes]
rs12105545	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712508	0.83[EUR][1000 genomes]
rs13029475	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13385408	0.89[EUR][1000 genomes]
rs13398345	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13406169	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13406184	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13410783	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs14291	0.84[EUR][1000 genomes]
rs1523786	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1533946	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1533947	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1533948	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1533949	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17019087	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17488036	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2022211	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2072533	0.91[EUR][1000 genomes]
rs2072534	0.91[EUR][1000 genomes]
rs2072535	0.90[EUR][1000 genomes]
rs2075226	0.92[EUR][1000 genomes]
rs2110986	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2110987	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2160403	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2160404	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34392255	0.89[EUR][1000 genomes]
rs34425257	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3755196	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770788	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770797	0.92[EUR][1000 genomes]
rs3770799	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770809	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3770811	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55700228	0.89[EUR][1000 genomes]
rs57670037	0.82[EUR][1000 genomes]
rs6728602	0.90[EUR][1000 genomes]
rs848610	0.86[EUR][1000 genomes]
rs848611	0.85[EUR][1000 genomes]
rs848612	0.83[EUR][1000 genomes]
rs848613	0.85[EUR][1000 genomes]
rs848614	0.82[EUR][1000 genomes]
rs848616	0.84[EUR][1000 genomes]
rs848619	0.85[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	0.90[EUR][1000 genomes]
rs848639	0.89[EUR][1000 genomes]
rs848640	0.86[EUR][1000 genomes]
rs848642	0.81[ASN][1000 genomes]
rs981355	0.81[EUR][1000 genomes]
rs9917316	0.91[EUR][1000 genomes]
rs9917318	0.82[AMR][1000 genomes];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
rs10178965	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr2:36750800-36783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:36762400-36783200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:36762800-36783800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:36763200-36784200	Strong transcription	HepG2	liver
8	chr2:36763200-36785200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:36764000-36790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:36764200-36783400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:36764200-36783800	Strong transcription	Fetal Intestine Large	intestine
12	chr2:36764400-36787200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:36764800-36791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:36766000-36791800	Weak transcription	Esophagus	oesophagus
15	chr2:36766400-36788600	Weak transcription	Fetal Brain Male	brain
16	chr2:36766800-36782800	Strong transcription	HMEC	breast
17	chr2:36766800-36783200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:36766800-36783400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:36769800-36790400	Weak transcription	Spleen	Spleen
20	chr2:36771000-36789000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:36771200-36788400	Weak transcription	Stomach Mucosa	stomach
22	chr2:36771400-36802800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:36771800-36782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:36772400-36783800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:36772600-36784200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:36772600-36784400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:36773600-36782800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:36773800-36782800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:36774200-36782800	Strong transcription	Liver	Liver
31	chr2:36774200-36784000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:36774200-36784200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:36774400-36789000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:36774600-36783200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:36776400-36783200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:36776600-36786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:36776600-36792600	Weak transcription	Right Ventricle	heart
38	chr2:36776600-36804800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:36776600-36804800	Weak transcription	Fetal Brain Female	brain
40	chr2:36776800-36782800	Strong transcription	Fetal Stomach	stomach
41	chr2:36777400-36786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:36777400-36786600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:36777400-36790600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:36777400-36795000	Weak transcription	Fetal Heart	heart
45	chr2:36777600-36783800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:36777800-36788000	Weak transcription	Brain Anterior Caudate	brain
47	chr2:36778200-36783400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:36778200-36783600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:36778200-36783600	Strong transcription	Dnd41	blood
50	chr2:36778200-36784800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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