Variant report

Variant	rs3772134
Chromosome Location	chr3:119388666-119388667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr3:119388600-119388767	HepG2	liver:	n/a	chr3:119388660-119388674
2	NFIC	chr3:119388620-119389224	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr3:119388527-119388738	HepG2	liver:	n/a	chr3:119388660-119388674

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119388635..119391771-chr3:119394131..119397043,3	MCF-7	breast:
2	chr3:119375861..119378454-chr3:119387094..119389806,2	K562	blood:
3	chr3:119377372..119379623-chr3:119387851..119390487,2	K562	blood:
4	chr3:119388646..119390230-chr3:119392331..119393863,2	K562	blood:
5	chr3:119383319..119384856-chr3:119387419..119389947,2	K562	blood:
6	chr3:119387433..119389444-chr3:119393932..119397317,5	K562	blood:
7	chr3:119387339..119389333-chr3:119392737..119395674,3	K562	blood:
8	chr3:119382052..119384819-chr3:119387419..119389641,2	K562	blood:

No data

Variant related genes	Relation type
POPDC2	TF binding region
ENSG00000138495	Chromatin interaction
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11720605	0.92[EUR][1000 genomes]
rs11914676	0.85[JPT][hapmap]
rs11923223	0.85[JPT][hapmap]
rs13062540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065543	0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13065893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1317259	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830291	0.85[JPT][hapmap]
rs1872432	0.85[JPT][hapmap]
rs1880040	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1880041	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046430	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280578	0.85[JPT][hapmap]
rs2629395	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2629397	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2629409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670296	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688629	0.85[JPT][hapmap]
rs2688631	0.85[JPT][hapmap]
rs2688633	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2692618	0.88[CEU][hapmap];0.90[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2698282	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3749417	0.95[ASN][1000 genomes]
rs4327424	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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687871	0.92[ASN][1000 genomes]
rs4688023	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688024	0.85[JPT][hapmap]
rs484809	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs523476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs572119	0.84[JPT][hapmap]
rs62265884	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6438541	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766563	0.90[JPT][hapmap]
rs6782253	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785698	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794484	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6794579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797667	0.95[YRI][hapmap]
rs6803814	0.80[JPT][hapmap]
rs6807079	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693397	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613999	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626940	0.90[JPT][hapmap]
rs7633444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8007	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs940181	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3772134	POPDC2	cis	cerebellum	SCAN
rs3772134	POPDC2	cis	lymphoblastoid	seeQTL
rs3772134	POPDC2	cis	multi-tissue	Pritchard
rs3772134	COX17	cis	lymphoblastoid	seeQTL
rs3772134	POPDC2	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
7	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
12	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:119373400-119388800	Weak transcription	Aorta	Aorta
14	chr3:119374800-119389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
17	chr3:119379200-119392400	Weak transcription	Gastric	stomach
18	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
19	chr3:119380000-119391800	Weak transcription	Lung	lung
20	chr3:119380000-119391800	Weak transcription	Ovary	ovary
21	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
22	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
23	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:119380400-119391000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:119381800-119389400	Weak transcription	A549	lung
27	chr3:119382000-119388800	Weak transcription	Right Atrium	heart
28	chr3:119382200-119390600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:119382400-119390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:119382400-119390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:119382400-119391000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
33	chr3:119382600-119388800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:119383800-119390600	Weak transcription	Brain Germinal Matrix	brain
36	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
37	chr3:119384000-119389000	Weak transcription	HSMM	muscle
38	chr3:119384000-119391800	Weak transcription	HSMMtube	muscle
39	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:119384200-119391600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
42	chr3:119384400-119388800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:119384400-119391000	Weak transcription	Fetal Intestine Small	intestine
44	chr3:119384400-119391200	Weak transcription	Fetal Kidney	kidney
45	chr3:119384400-119391200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:119384600-119388800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:119384600-119388800	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:119384600-119391600	Weak transcription	K562	blood
49	chr3:119384600-119391800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:119384600-119392400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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