Variant report

Variant	rs1879511
Chromosome Location	chr3:112021896-112021897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:112021224-112022933	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr3:112021890-112022672	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:112021832-112022401	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr3:112021868-112022946	H1-hESC	embryonic stem cell:	n/a	n/a
5	POU5F1	chr3:112021866-112022496	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:112021831-112022258	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:112020833-112022650	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr3:112021596-112022928	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTBP2	chr3:112021346-112022312	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr3:112021860-112022010	HCPEpiC	choroid plexus:	n/a	n/a
11	RAD21	chr3:112021872-112022331	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr3:112021863-112023047	H1-hESC	embryonic stem cell:	n/a	chr3:112022141-112022152
13	SPI1	chr3:112021605-112021903	GM12878	blood:	n/a	n/a
14	SP1	chr3:112021821-112022488	H1-hESC	embryonic stem cell:	n/a	chr3:112022141-112022152
15	SPI1	chr3:112021564-112021908	GM12891	blood:	n/a	n/a
16	TAF1	chr3:112021840-112022466	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr3:112021873-112022512	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD2	chr3:112021818-112022916	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:112021880-112022163	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF143	chr3:112021133-112023008	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr3:112021808-112022350	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr3:112021849-112022430	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF7	chr3:112021843-112022422	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:112021187-112022691	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10804500	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934166	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934167	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934169	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934170	0.81[EUR][1000 genomes]
rs11708769	0.81[EUR][1000 genomes]
rs11710561	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11712036	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719721	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917566	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917581	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629421	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630238	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630278	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633029	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634619	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12635015	0.81[EUR][1000 genomes]
rs12635872	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12639474	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13069751	0.85[ASN][1000 genomes]
rs1317243	0.81[CHD][hapmap]
rs16859469	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859507	0.81[EUR][1000 genomes]
rs1814987	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2895395	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2895396	0.81[EUR][1000 genomes]
rs4355253	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4355254	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682101	0.82[ASN][1000 genomes]
rs57025230	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57661530	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58425909	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59202208	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59744939	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62264124	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62278831	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278832	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278833	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278834	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278835	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278837	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278838	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278839	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278841	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62278842	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278846	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62278847	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62278848	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278849	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278850	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278853	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62278854	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278855	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62278856	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764384	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787841	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788309	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6789161	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801708	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801739	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72950242	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72950273	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952411	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72952437	0.81[EUR][1000 genomes]
rs7639471	1.00[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639794	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7653490	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834347	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9863371	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867245	0.81[EUR][1000 genomes]
rs9868582	0.94[ASN][1000 genomes]
rs9876973	0.84[ASN][1000 genomes]
rs9990215	0.81[CHB][hapmap]
rs9990216	0.81[CHD][hapmap]
rs9990220	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112013400-112022200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:112016600-112022000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:112016600-112022400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:112017000-112022200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:112017200-112022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:112017600-112022000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:112017600-112022200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:112017800-112022000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:112017800-112022200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:112018000-112022000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:112018000-112022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:112018000-112022000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:112018000-112022000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:112018000-112022200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:112020800-112022000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:112021000-112022000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:112021000-112022000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:112021000-112022200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:112021000-112022400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:112021000-112022400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr3:112021000-112023000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:112021200-112022000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:112021200-112022200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:112021200-112022200	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:112021200-112022200	Weak transcription	Spleen	Spleen
26	chr3:112021200-112022400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:112021200-112023400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr3:112021400-112022000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:112021400-112022000	Active TSS	NHDF-Ad	bronchial
30	chr3:112021400-112022200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:112021400-112022200	Active TSS	Brain Anterior Caudate	brain
32	chr3:112021400-112022600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:112021400-112023000	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:112021400-112023200	Active TSS	Colon Smooth Muscle	Colon
35	chr3:112021400-112023200	Flanking Active TSS	Fetal Thymus	thymus
36	chr3:112021400-112023400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr3:112021400-112025200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112021600-112022000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:112021600-112022000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:112021600-112022000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:112021600-112022000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:112021600-112022000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:112021600-112022000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr3:112021600-112022000	Enhancers	Fetal Brain Male	brain
45	chr3:112021600-112022000	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr3:112021600-112022000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr3:112021600-112022000	Enhancers	GM12878-XiMat	blood
48	chr3:112021600-112022200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:112021600-112022200	Active TSS	Brain Substantia Nigra	brain
50	chr3:112021600-112022200	Active TSS	Duodenum Smooth Muscle	Duodenum

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