Variant report

Variant	rs6810125
Chromosome Location	chr3:56646820-56646821
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

Variant related genes	Relation type
CCDC66	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]
rs11130522	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1388252	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1491162	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1491167	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17216678	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17216712	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17216754	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288866	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288873	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306930	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306931	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276465	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276467	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276469	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4292200	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56758331	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57861120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58457441	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59835031	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59897254	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60606369	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61456176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61654248	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61747994	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62249737	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62251182	0.92[EUR][1000 genomes]
rs62251183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251186	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62251188	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251190	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251192	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251193	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251197	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251228	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251229	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251230	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251233	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251235	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251238	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251240	0.81[EUR][1000 genomes]
rs62251241	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251244	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251245	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254329	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255965	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62255967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255969	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255973	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255977	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255978	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62256014	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256019	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782254	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6788512	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802548	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73075746	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081816	0.92[EUR][1000 genomes]
rs73081836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73083715	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083725	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635945	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955247	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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:126 , 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	chr3:56640600-56647200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:56640600-56647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
19	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:56640800-56647000	Weak transcription	Liver	Liver
22	chr3:56640800-56647200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:56640800-56647400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:56640800-56647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:56640800-56647400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:56640800-56647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:56640800-56647600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:56640800-56647800	Weak transcription	Dnd41	blood
29	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:56640800-56649400	Weak transcription	Osteobl	bone
31	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
32	chr3:56640800-56650400	Weak transcription	NHLF	lung
33	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
34	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:56641200-56647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:56641200-56647000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
41	chr3:56643400-56647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:56644000-56647000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:56644000-56647400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:56644400-56647400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:56644400-56647400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:56644400-56647800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
49	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:56644600-56647200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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