Variant report

Variant	rs1564177
Chromosome Location	chr3:42815245-42815246
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	RFX5	chr3:42813993-42815422	IMR90	lung:	n/a	chr3:42814739-42814754
2	MXI1	chr3:42814055-42815533	SK-N-SH	brain:	n/a	n/a
3	REST	chr3:42814206-42815272	H1-neurons	neurons:	n/a	chr3:42814242-42814255 chr3:42814344-42814351
4	MXI1	chr3:42813972-42815298	IMR90	lung:	n/a	n/a
5	RFX5	chr3:42814215-42815565	SK-N-SH	brain:	n/a	chr3:42814739-42814754

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42812718..42815694-chr3:42844363..42847706,3	K562	blood:

Variant related genes	Relation type
CCDC13	TF binding region
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11129971	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35426298	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5027058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778695	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.93[AFR][1000 genomes]
rs7648688	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	0.85[AMR][1000 genomes]

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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42813000-42821400	Weak transcription	Dnd41	blood
2	chr3:42813000-42821800	Weak transcription	HepG2	liver
3	chr3:42814200-42815400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:42814200-42815400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr3:42814200-42815400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr3:42814200-42815400	Active TSS	NHLF	lung
7	chr3:42814400-42815400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:42814600-42815400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:42814600-42815400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:42814600-42815400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:42814600-42815400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:42814600-42815400	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:42814600-42815400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:42814600-42815400	Active TSS	Stomach Smooth Muscle	stomach
15	chr3:42814600-42815400	Active TSS	HUVEC	blood vessel
16	chr3:42814600-42815400	Active TSS	NHDF-Ad	bronchial
17	chr3:42814600-42822200	Weak transcription	Fetal Heart	heart
18	chr3:42814800-42815400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:42814800-42819200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:42814800-42823800	Weak transcription	Lung	lung
21	chr3:42814800-42824800	Weak transcription	Gastric	stomach
22	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
23	chr3:42815000-42815400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr3:42815000-42815400	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:42815000-42815400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:42815000-42815400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:42815000-42815400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr3:42815000-42815400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:42815000-42815400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:42815000-42820200	Weak transcription	Pancreas	Pancrea
31	chr3:42815000-42821400	Weak transcription	Esophagus	oesophagus
32	chr3:42815000-42823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:42815000-42824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:42815200-42815400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:42815200-42815400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr3:42815200-42815400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:42815200-42815400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:42815200-42815400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:42815200-42815400	Enhancers	Adipose Nuclei	Adipose
41	chr3:42815200-42815400	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:42815200-42815400	Enhancers	Brain Germinal Matrix	brain
43	chr3:42815200-42815400	Enhancers	Colon Smooth Muscle	Colon
44	chr3:42815200-42815400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:42815200-42815400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:42815200-42815400	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:42815200-42815400	Enhancers	Osteobl	bone
48	chr3:42815200-42815600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:42815200-42815600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:42815200-42815600	Enhancers	Primary T helper cells PMA-I stimulated	--

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