Variant report

Variant	rs9846575
Chromosome Location	chr3:56647366-56647367
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	POLR2A	chr3:56646351-56647657	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:56646605-56647526	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:56647004-56647598	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56647300..56648856-chr3:56648916..56651486,2	K562	blood:

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130524	0.84[AFR][1000 genomes]
rs13316272	1.00[AMR][1000 genomes]
rs13320990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13326525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28493474	0.84[AFR][1000 genomes]
rs28605592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28846202	0.84[AFR][1000 genomes]
rs9817151	1.00[AMR][1000 genomes]
rs9821740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9824415	1.00[AMR][1000 genomes]
rs9827937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9848723	0.84[AFR][1000 genomes]
rs9853548	0.97[AFR][1000 genomes]
rs9861624	1.00[AMR][1000 genomes]
rs9864263	1.00[AMR][1000 genomes]
rs9867688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9873327	1.00[AFR][1000 genomes]
rs9877962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9883323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9985426	1.00[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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
9	chr3:56629000-56648000	Weak transcription	NH-A	brain
10	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
11	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
14	chr3:56640000-56650000	Weak transcription	HMEC	breast
15	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:56640600-56647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
18	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:56640800-56647400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:56640800-56647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:56640800-56647400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:56640800-56647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:56640800-56647600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:56640800-56647800	Weak transcription	Dnd41	blood
26	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:56640800-56649400	Weak transcription	Osteobl	bone
28	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
29	chr3:56640800-56650400	Weak transcription	NHLF	lung
30	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
31	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
36	chr3:56643400-56647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:56644000-56647400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:56644400-56647400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:56644400-56647400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:56644400-56647800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
43	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:56644600-56647600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:56644600-56647600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:56644600-56647600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:56644600-56647800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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