Variant report

Variant	rs16859897
Chromosome Location	chr3:112362600-112362601
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	MAX	chr3:112362554-112362862	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr3:112362561-112362898	GM12878	blood:	n/a	n/a
3	RAD21	chr3:112361530-112362668	IMR90	lung:	n/a	chr3:112361927-112361946
4	EP300	chr3:112361556-112362839	A549	lung:	n/a	chr3:112361594-112361603
5	E2F6	chr3:112362416-112363295	A549	lung:	n/a	n/a
6	CTCF	chr3:112361227-112362721	A549	lung:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
7	MAX	chr3:112362492-112363030	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:112361541-112363802	A549	lung:	n/a	n/a
9	E2F6	chr3:112362569-112363066	H1-hESC	embryonic stem cell:	n/a	n/a
10	GATA3	chr3:112361558-112362604	A549	lung:	n/a	chr3:112362500-112362510
11	REST	chr3:112361764-112362696	A549	lung:	n/a	chr3:112362341-112362354
12	E2F6	chr3:112362431-112363208	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr3:112361493-112362934	A549	lung:	n/a	n/a
14	SMC3	chr3:112361432-112362736	SK-N-SH	brain:	n/a	chr3:112361928-112361942
15	MAX	chr3:112362496-112363172	A549	lung:	n/a	n/a
16	BHLHE40	chr3:112362590-112362895	GM12878	blood:	n/a	n/a
17	MAX	chr3:112362597-112363010	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112361784..112364489-chr3:112737772..112739628,2	MCF-7	breast:
2	chr3:112362227..112366265-chr3:112408651..112412487,6	MCF-7	breast:
3	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
4	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
5	chr3:112361572..112365675-chr3:112707892..112711353,4	MCF-7	breast:
6	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000163608	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163606	Chromatin interaction
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10511317	1.00[AFR][1000 genomes]
rs1072896	1.00[AFR][1000 genomes]
rs12630906	1.00[AFR][1000 genomes]
rs12634199	1.00[AFR][1000 genomes]
rs12634229	0.83[ASN][1000 genomes]
rs12637057	0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12637953	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs13059364	1.00[AFR][1000 genomes]
rs13063173	1.00[AFR][1000 genomes]
rs13078401	1.00[AFR][1000 genomes]
rs13079599	1.00[AFR][1000 genomes]
rs13081265	1.00[AFR][1000 genomes]
rs13086960	1.00[AFR][1000 genomes]
rs13096943	1.00[AFR][1000 genomes]
rs16845068	1.00[AFR][1000 genomes]
rs16845073	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs16859758	1.00[AFR][1000 genomes]
rs16859849	1.00[AFR][1000 genomes]
rs16859890	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16859911	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16859916	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16859930	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16859961	1.00[AFR][1000 genomes]
rs28364588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28364589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28364604	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34080815	1.00[AFR][1000 genomes]
rs34541731	1.00[AFR][1000 genomes]
rs34829517	1.00[AFR][1000 genomes]
rs34889961	1.00[AFR][1000 genomes]
rs34949685	1.00[AFR][1000 genomes]
rs34962178	1.00[AFR][1000 genomes]
rs35263368	1.00[AFR][1000 genomes]
rs35526995	1.00[AFR][1000 genomes]
rs35931975	1.00[AFR][1000 genomes]
rs36045008	1.00[AFR][1000 genomes]
rs36153507	1.00[AFR][1000 genomes]
rs3736269	1.00[AFR][1000 genomes]
rs3773701	1.00[AFR][1000 genomes]
rs3773704	1.00[AFR][1000 genomes]
rs56721759	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60646325	1.00[AFR][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66546764	1.00[AFR][1000 genomes]
rs66791711	1.00[AFR][1000 genomes]
rs67021100	1.00[AFR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes]
rs71317507	1.00[AFR][1000 genomes]
rs71317508	1.00[AFR][1000 genomes]
rs73229350	1.00[AFR][1000 genomes]
rs73229353	1.00[AFR][1000 genomes]
rs7640793	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:112358600-112365400	Weak transcription	Lung	lung
3	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112359000-112363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:112359400-112363200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:112359600-112362800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:112359600-112365400	Weak transcription	Pancreas	Pancrea
8	chr3:112359800-112362600	Weak transcription	Esophagus	oesophagus
9	chr3:112359800-112362800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:112359800-112363000	Enhancers	HMEC	breast
11	chr3:112359800-112363400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:112360200-112363600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:112360600-112363000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:112360600-112363400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:112360600-112363600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:112360600-112363800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:112360800-112363400	Enhancers	HSMM	muscle
18	chr3:112360800-112365200	Weak transcription	Psoas Muscle	Psoas
19	chr3:112360800-112365600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:112360800-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:112361000-112362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:112361000-112362600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:112361000-112363200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:112361000-112363400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:112361000-112365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:112361000-112365800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:112361200-112363600	Enhancers	NHLF	lung
28	chr3:112361600-112362600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:112361600-112362800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112361600-112362800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:112361600-112362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:112361600-112363200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:112361800-112362600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:112361800-112362800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:112361800-112363000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:112361800-112363600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:112361800-112363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:112362000-112362600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:112362000-112362600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:112362000-112362800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr3:112362000-112362800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:112362000-112362800	Enhancers	K562	blood
43	chr3:112362000-112362800	Enhancers	NH-A	brain
44	chr3:112362000-112363000	Enhancers	Primary T cells from cord blood	blood
45	chr3:112362000-112363000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:112362000-112363200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:112362000-112363400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:112362000-112363600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr3:112362000-112363600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:112362200-112362600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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