Variant report

Variant	rs3779989
Chromosome Location	chr8:124429923-124429924
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	POLR2A	chr8:124428357-124429947	Raji	blood:	n/a	n/a
2	CTCF	chr8:124429880-124430030	SAEC	small airway:	n/a	n/a
3	RCOR1	chr8:124429838-124430069	K562	blood:	n/a	n/a
4	CHD2	chr8:124429918-124430078	HepG2	liver:	n/a	n/a
5	POLR2A	chr8:124428826-124429937	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr8:124428326-124429942	GM18951	blood:	n/a	n/a
7	POLR2A	chr8:124429511-124430024	GM12892	blood:	n/a	n/a
8	HDAC2	chr8:124429750-124430123	K562	blood:	n/a	n/a
9	POLR2A	chr8:124429735-124429990	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr8:124428340-124430117	K562	blood:	n/a	n/a
11	MAX	chr8:124428212-124430255	MCF-7	breast:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
12	POLR2A	chr8:124429624-124429978	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr8:124428129-124430094	MCF-7	breast:	n/a	n/a
14	POLR2A	chr8:124428266-124430227	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr8:124428252-124429947	K562	blood:	n/a	n/a
16	POLR2A	chr8:124428329-124430384	GM12878	blood:	n/a	n/a
17	REST	chr8:124428259-124430091	H1-neurons	neurons:	n/a	chr8:124428978-124428991 chr8:124428917-124428930 chr8:124429934-124429952 chr8:124429406-124429419
18	MAZ	chr8:124428225-124429925	IMR90	lung:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
19	EGR1	chr8:124428255-124429923	MCF-7	breast:	n/a	chr8:124428972-124428982 chr8:124428918-124428928 chr8:124428979-124428994 chr8:124429181-124429190 chr8:124428801-124428814 chr8:124428980-124428993 chr8:124428917-124428927
20	MXI1	chr8:124428051-124430416	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr8:124429683-124430115	K562	blood:	n/a	n/a
22	RUNX3	chr8:124429170-124430032	GM12878	blood:	n/a	n/a
23	HA-E2F1	chr8:124428281-124430035	MCF-7	breast:	n/a	chr8:124428877-124428889 chr8:124428913-124428923 chr8:124429177-124429186 chr8:124428877-124428888
24	MAZ	chr8:124428312-124429997	K562	blood:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
25	POLR2A	chr8:124429741-124430398	PFSK-1	brain:	n/a	n/a
26	YY1	chr8:124429752-124429938	K562	blood:	n/a	n/a
27	POLR2A	chr8:124428252-124430009	Hela-S3	cervix:	n/a	n/a
28	MAZ	chr8:124428428-124429925	Hela-S3	cervix:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
29	ELF1	chr8:124428282-124429928	MCF-7	breast:	n/a	chr8:124428728-124428737 chr8:124428727-124428738 chr8:124428729-124428738 chr8:124428727-124428738 chr8:124428972-124428984 chr8:124428918-124428930
30	POLR2A	chr8:124429558-124430033	GM12892	blood:	n/a	n/a
31	MXI1	chr8:124428093-124430006	IMR90	lung:	n/a	n/a
32	POLR2A	chr8:124427524-124430634	HepG2	liver:	n/a	n/a
33	POLR2A	chr8:124428831-124430062	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr8:124428343-124429993	K562	blood:	n/a	n/a
35	WRNIP1	chr8:124429724-124430042	GM12878	blood:	n/a	n/a
36	MAX	chr8:124428308-124430038	HepG2	liver:	n/a	chr8:124429308-124429318 chr8:124428917-124428927
37	YY1	chr8:124429660-124430059	HepG2	liver:	n/a	n/a
38	POLR2A	chr8:124428306-124430043	HepG2	liver:	n/a	n/a
39	POLR2A	chr8:124428831-124430170	GM12892	blood:	n/a	n/a
40	POLR2A	chr8:124428273-124430254	GM12891	blood:	n/a	n/a
41	POLR2A	chr8:124428341-124430002	GM18505	blood:	n/a	n/a
42	POLR2A	chr8:124429690-124429972	Hela-S3	cervix:	n/a	n/a
43	BHLHE40	chr8:124429827-124430025	K562	blood:	n/a	n/a
44	YY1	chr8:124429677-124430046	GM12878	blood:	n/a	n/a
45	MTA3	chr8:124428775-124430069	GM12878	blood:	n/a	n/a
46	HDAC2	chr8:124429787-124430043	K562	blood:	n/a	n/a
47	HCFC1	chr8:124428081-124430199	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr8:124428349-124429972	GM12892	blood:	n/a	n/a
49	POLR2A	chr8:124428174-124430138	H1-hESC	embryonic stem cell:	n/a	n/a
50	RUNX3	chr8:124429675-124430132	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:124429815..124432313-chr8:124778028..124780178,2	K562	blood:
2	chr8:124283829..124288838-chr8:124426117..124430573,9	K562	blood:
3	chr8:124285038..124289042-chr8:124427512..124430569,10	MCF-7	breast:
4	chr8:124429705..124433349-chr8:124436919..124438611,3	K562	blood:
5	chr8:124283849..124288367-chr8:124426037..124430184,7	K562	blood:
6	chr8:124411247..124413629-chr8:124428301..124430441,2	K562	blood:
7	chr8:124406056..124410111-chr8:124427174..124433258,8	MCF-7	breast:
8	chr8:124253290..124255259-chr8:124427452..124430915,4	MCF-7	breast:
9	chr8:124287117..124289356-chr8:124428879..124431490,3	MCF-7	breast:
10	chr8:124406688..124410730-chr8:124426992..124430866,9	K562	blood:
11	chr8:124404505..124411576-chr8:124423647..124430734,19	MCF-7	breast:
12	chr8:124428663..124430757-chr8:124778757..124780951,2	K562	blood:
13	chr8:124405499..124410730-chr8:124426606..124431705,19	K562	blood:
14	chr11:62623530..62624100-chr8:124428998..124429986,2	Hela-S3	cervix:
15	chr8:124427319..124431344-chr8:124440107..124444172,5	MCF-7	breast:
16	chr1:108743710..108745219-chr8:124429078..124431227,2	MCF-7	breast:
17	chr8:124427993..124430634-chr8:124780278..124783215,3	MCF-7	breast:

Variant related genes	Relation type
ATAD2	TF binding region
ENSG00000168003	Chromatin interaction
ENSG00000189376	Chromatin interaction
ENSG00000165156	Chromatin interaction
ENSG00000176853	Chromatin interaction
ENSG00000156795	Chromatin interaction
ENSG00000254294	Chromatin interaction
ENSG00000156802	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10111271	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956126	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956131	0.80[EUR][1000 genomes]
rs11774702	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11776589	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783637	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787093	0.91[EUR][1000 genomes]
rs12543979	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12707901	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13266016	0.80[EUR][1000 genomes]
rs3779985	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs3779991	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3857957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4006576	0.91[EUR][1000 genomes]
rs4870851	0.96[EUR][1000 genomes]
rs4871366	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871367	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871368	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871370	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4871371	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4871373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4871377	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62519216	0.89[EUR][1000 genomes]
rs6470146	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6981304	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6982598	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6986525	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6986901	0.82[EUR][1000 genomes]
rs6987599	0.82[EUR][1000 genomes]
rs7012343	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72724211	0.88[ASN][1000 genomes]
rs72724214	0.88[ASN][1000 genomes]
rs7817573	0.83[EUR][1000 genomes]
rs7833321	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7836626	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7836880	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840703	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7844004	0.85[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	nsv831449	chr8:124276685-124471740	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3415547	chr8:124420820-124444289	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3779989	WDYHV1	cis	Heart Left Ventricle	GTEx
rs3779989	WDYHV1	cis	parietal	SCAN
rs3779989	WDYHV1	cis	lymphoblastoid	seeQTL
rs3779989	MRPL13	cis	cerebellum	SCAN
rs3779989	WDYHV1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124427600-124430200	Active TSS	A549	lung
2	chr8:124428000-124430000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:124428000-124430000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr8:124428200-124430000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr8:124428200-124430000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:124428200-124430000	Active TSS	Ovary	ovary
7	chr8:124428200-124430200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:124428400-124430000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:124428400-124430000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:124428400-124430000	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr8:124428400-124430000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:124428400-124430400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr8:124428600-124430000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr8:124428600-124430000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr8:124428600-124430200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr8:124429200-124430000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr8:124429200-124430000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr8:124429200-124430000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:124429200-124430000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr8:124429400-124430000	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr8:124429400-124430000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr8:124429400-124430000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:124429400-124430000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr8:124429400-124430000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr8:124429400-124430000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr8:124429400-124430000	Flanking Active TSS	Liver	Liver
27	chr8:124429400-124430000	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr8:124429400-124430000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr8:124429400-124430000	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr8:124429400-124430000	Flanking Active TSS	Fetal Stomach	stomach
31	chr8:124429400-124430000	Flanking Active TSS	HUVEC	blood vessel
32	chr8:124429400-124430000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr8:124429400-124430200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr8:124429400-124430200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:124429400-124430200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr8:124429400-124430200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:124429400-124430200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr8:124429400-124430200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr8:124429400-124430400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:124429400-124430400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr8:124429600-124430000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr8:124429600-124430000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr8:124429600-124430000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:124429600-124430000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr8:124429600-124430000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr8:124429600-124430000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr8:124429600-124430000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr8:124429600-124430000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr8:124429600-124430000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr8:124429600-124430000	Flanking Active TSS	Brain Cingulate Gyrus	brain

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