Variant report

Variant	rs4944920
Chromosome Location	chr11:74347434-74347435
allele	C/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	GATA2	chr11:74347367-74348152	HUVEC	blood vessel:	n/a	chr11:74347584-74347591 chr11:74347829-74347838 chr11:74347577-74347598 chr11:74347584-74347591 chr11:74347584-74347591 chr11:74347580-74347596
2	GATA3	chr11:74347411-74347761	SH-SY5Y	brain:	n/a	chr11:74347584-74347591 chr11:74347577-74347598 chr11:74347584-74347591 chr11:74347584-74347591 chr11:74347580-74347596
3	GATA3	chr11:74347195-74348208	SK-N-SH	brain:	n/a	chr11:74347584-74347591 chr11:74347829-74347838 chr11:74347577-74347598 chr11:74347584-74347591 chr11:74347584-74347591 chr11:74347580-74347596
4	STAT3	chr11:74347410-74347984	MCF10A-Er-Src	breast:	n/a	chr11:74347830-74347839 chr11:74347912-74347920 chr11:74347831-74347840
5	GATA3	chr11:74347314-74348147	SK-N-SH	brain:	n/a	chr11:74347584-74347591 chr11:74347829-74347838 chr11:74347577-74347598 chr11:74347584-74347591 chr11:74347584-74347591 chr11:74347580-74347596
6	FOS	chr11:74347404-74348121	MCF10A-Er-Src	breast:	n/a	chr11:74347831-74347840 chr11:74347829-74347841 chr11:74347830-74347839 chr11:74347831-74347839 chr11:74347829-74347840 chr11:74347935-74347943 chr11:74347831-74347838 chr11:74347936-74347943
7	CTCF	chr11:74347300-74347450	HMF	breast:	n/a	n/a
8	YY1	chr11:74347415-74348179	SK-N-SH	brain:	n/a	chr11:74347957-74347966
9	JUND	chr11:74347134-74348284	SK-N-SH	brain:	n/a	chr11:74347831-74347840 chr11:74347829-74347841 chr11:74347830-74347839 chr11:74347831-74347839 chr11:74347935-74347943 chr11:74347831-74347838 chr11:74347829-74347840 chr11:74347936-74347943

No.	Distal block	Cell Line	Cell type
1	chr11:74342999..74345497-chr11:74347064..74349152,2	K562	blood:
2	chr11:74333645..74336411-chr11:74344978..74348426,3	K562	blood:
3	chr11:74346357..74348361-chr11:74458925..74461274,2	MCF-7	breast:
4	chr11:74346915..74349082-chr11:74357415..74360108,2	MCF-7	breast:
5	chr11:74346179..74347849-chr11:74403237..74405199,2	MCF-7	breast:
6	chr11:74343993..74348455-chr11:74350438..74354140,4	K562	blood:
7	chr11:74340115..74342443-chr11:74346109..74347892,2	K562	blood:
8	chr11:74346326..74348110-chr11:74428577..74431103,2	MCF-7	breast:
9	chr11:74333645..74336229-chr11:74343900..74348454,4	K562	blood:

Variant related genes	Relation type
POLD3	TF binding region
ENSG00000054938	Chromatin interaction
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10751239	0.82[ASN][1000 genomes]
rs10793095	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793102	0.85[CEU][hapmap]
rs10857	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[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899010	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236154	0.84[ASN][1000 genomes]
rs12421418	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1433969	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1433972	0.83[MEX][hapmap]
rs1893362	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1944935	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1971114	0.84[ASN][1000 genomes]
rs2298572	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417306	0.83[MEX][hapmap]
rs4514450	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4584608	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4627114	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944048	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944049	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944054	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944055	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944056	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944057	0.82[ASN][1000 genomes]
rs4944904	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4944911	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944916	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944928	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944929	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944930	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944931	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944936	1.00[ASW][hapmap]
rs6592568	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6592574	0.97[ASN][1000 genomes]
rs6592575	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592576	0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592578	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592580	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592582	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106984	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111251	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7111273	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118314	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7122810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126573	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126957	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7127499	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7127628	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127630	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127668	0.87[ASN][1000 genomes]
rs7130694	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131096	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924701	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925747	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929876	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7933770	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7934301	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934321	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7934742	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7935057	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935260	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7937232	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7938931	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7947345	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952661	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9651760	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651761	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4944920	POLD3	cis	cerebellum	SCAN
rs4944920	PPFIA1	cis	parietal	SCAN
rs4944920	UCP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74304600-74373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:74304800-74357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:74304800-74361400	Weak transcription	Colonic Mucosa	Colon
4	chr11:74310200-74352400	Weak transcription	Fetal Brain Male	brain
5	chr11:74314000-74370200	Weak transcription	Psoas Muscle	Psoas
6	chr11:74317200-74352200	Weak transcription	Aorta	Aorta
7	chr11:74319200-74366000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:74321600-74364800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:74322200-74357400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:74323000-74356800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:74325000-74351600	Weak transcription	Right Ventricle	heart
12	chr11:74325200-74351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:74325600-74350600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:74330200-74351600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:74331400-74383400	Weak transcription	Brain Substantia Nigra	brain
16	chr11:74332200-74348800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:74335200-74356800	Strong transcription	Fetal Thymus	thymus
18	chr11:74335200-74357000	Strong transcription	Dnd41	blood
19	chr11:74336000-74354400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:74336200-74358200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:74336600-74354400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:74336800-74353800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:74336800-74354600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:74337800-74353800	Strong transcription	Primary B cells from cord blood	blood
25	chr11:74339200-74356000	Weak transcription	Fetal Heart	heart
26	chr11:74339400-74356000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:74340000-74348000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:74340000-74364200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:74340600-74351200	Weak transcription	HSMM	muscle
30	chr11:74343000-74354800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:74343200-74350200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:74343400-74349400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:74343400-74354800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:74343600-74348200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:74343600-74349600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:74344000-74354000	Strong transcription	Fetal Intestine Large	intestine
37	chr11:74344200-74348600	Strong transcription	Fetal Muscle Leg	muscle
38	chr11:74344200-74353200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:74344200-74353800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:74344200-74363200	Strong transcription	Primary T cells from cord blood	blood
41	chr11:74344400-74348400	Genic enhancers	A549	lung
42	chr11:74344400-74353400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:74344600-74347800	Weak transcription	HSMMtube	muscle
44	chr11:74344600-74349000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr11:74344800-74363400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:74345200-74348000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr11:74345400-74347600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:74345400-74347600	Strong transcription	Brain Angular Gyrus	brain
49	chr11:74345400-74348200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:74345600-74347600	Strong transcription	Brain Inferior Temporal Lobe	brain

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