Variant report

Variant	rs6905453
Chromosome Location	chr6:143167564-143167565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143166680..143169916-chr6:143203323..143206412,3	MCF-7	breast:
2	chr6:143167088..143169502-chr6:143267608..143269824,2	MCF-7	breast:
3	chr6:143163087..143164767-chr6:143165602..143167738,2	K562	blood:
4	chr6:143166711..143168241-chr6:143264865..143267467,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11155265	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11969311	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190015	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12190804	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12192692	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194338	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12194808	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12196693	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12199711	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12201734	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12201987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12205948	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12208876	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12210048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12210301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214573	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17444447	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2142938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184364	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876528	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349826	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4492208	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62430707	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430709	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62430712	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62430713	0.87[EUR][1000 genomes]
rs62432360	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62432362	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6910072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912129	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6925118	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72990282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72995085	0.80[EUR][1000 genomes]
rs7758383	0.90[ASN][1000 genomes]
rs972119	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998313	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143163000-143167800	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr6:143164200-143167600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr6:143164200-143168400	Enhancers	Fetal Thymus	thymus
4	chr6:143165000-143168400	Enhancers	Dnd41	blood
5	chr6:143165200-143168200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:143165200-143168400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:143165200-143169000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:143165400-143167600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr6:143165400-143168200	Flanking Active TSS	Osteobl	bone
10	chr6:143165400-143168600	Flanking Active TSS	NHDF-Ad	bronchial
11	chr6:143165600-143167600	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr6:143165600-143168400	Enhancers	Small Intestine	intestine
13	chr6:143165600-143168600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:143165600-143168600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:143165600-143168600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr6:143165600-143168600	Flanking Active TSS	NHLF	lung
17	chr6:143165800-143168400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:143165800-143168400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:143165800-143168400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:143165800-143168600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:143165800-143168800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:143165800-143169800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:143166000-143167800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:143166000-143168400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr6:143166000-143168400	Enhancers	Lung	lung
26	chr6:143166000-143168400	Enhancers	Pancreas	Pancrea
27	chr6:143166000-143168400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:143166000-143168400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr6:143166000-143169000	Enhancers	Hela-S3	cervix
30	chr6:143166200-143168800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:143166200-143169400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:143166400-143167600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:143166400-143167600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:143166400-143167600	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr6:143166400-143167600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:143166400-143167600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:143166400-143167600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr6:143166400-143167600	Active TSS	A549	lung
39	chr6:143166400-143167600	Flanking Active TSS	HUVEC	blood vessel
40	chr6:143166400-143167600	Flanking Active TSS	NHEK	skin
41	chr6:143166400-143167800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:143166400-143167800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:143166400-143168800	Flanking Active TSS	NH-A	brain
44	chr6:143166600-143167600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr6:143166600-143167600	Flanking Active TSS	Fetal Brain Female	brain
46	chr6:143166600-143167600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:143166600-143168200	Flanking Active TSS	GM12878-XiMat	blood
48	chr6:143166600-143168400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:143166600-143168400	Enhancers	Ovary	ovary
50	chr6:143166600-143168400	Flanking Active TSS	HSMM	muscle

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