Variant report

Variant	rs576657
Chromosome Location	chr6:143124594-143124595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143122037..143125771-chr6:143264772..143267581,3	MCF-7	breast:
2	chr6:143118967..143121950-chr6:143122825..143125475,2	K562	blood:
3	chr6:143119457..143121127-chr6:143123528..143126116,2	K562	blood:
4	chr6:143116694..143119328-chr6:143121007..143124845,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11155264	0.86[ASN][1000 genomes]
rs197494	0.87[JPT][hapmap];0.81[YRI][hapmap]
rs197496	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs197497	0.87[JPT][hapmap];0.86[YRI][hapmap]
rs197511	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs2328388	0.85[ASN][1000 genomes]
rs472185	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472288	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473497	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478768	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487754	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491414	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491953	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492156	0.92[ASN][1000 genomes]
rs494038	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494954	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511565	0.82[ASN][1000 genomes]
rs512808	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516300	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs519874	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525928	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527870	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs533117	0.87[ASN][1000 genomes]
rs533173	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550149	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552004	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs552928	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557004	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561642	0.96[ASN][1000 genomes]
rs576760	0.86[ASN][1000 genomes]
rs9376708	0.82[ASN][1000 genomes]
rs9386009	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403407	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	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
3	nsv1019558	chr6:143121577-143154554	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143096200-143140800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:143103600-143124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:143103800-143125400	Weak transcription	Fetal Thymus	thymus
4	chr6:143105800-143140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:143106000-143128200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:143106000-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:143112200-143139400	Weak transcription	HepG2	liver
8	chr6:143113200-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:143114200-143140800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:143116000-143125400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:143116000-143139600	Weak transcription	Small Intestine	intestine
12	chr6:143116200-143132200	Weak transcription	Fetal Brain Female	brain
13	chr6:143117000-143129400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:143117000-143140800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:143118000-143126200	Weak transcription	Right Ventricle	heart
16	chr6:143118000-143132200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:143118000-143137600	Weak transcription	Right Atrium	heart
18	chr6:143119600-143129600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:143119800-143126200	Weak transcription	Left Ventricle	heart
20	chr6:143119800-143126200	Weak transcription	Thymus	Thymus
21	chr6:143119800-143130000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:143120400-143125400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:143121000-143126200	Weak transcription	Aorta	Aorta
24	chr6:143121000-143133000	Weak transcription	Pancreas	Pancrea
25	chr6:143121200-143125600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:143121200-143138400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:143121400-143126000	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:143121600-143129400	Weak transcription	Brain Anterior Caudate	brain
29	chr6:143122800-143126600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:143123000-143125200	Enhancers	HMEC	breast
31	chr6:143123000-143125800	Weak transcription	Primary T cells from cord blood	blood
32	chr6:143123400-143125000	Weak transcription	Primary B cells from cord blood	blood
33	chr6:143123400-143126200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:143123400-143128400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr6:143123400-143132000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:143123400-143140600	Weak transcription	HSMM	muscle
37	chr6:143123400-143144000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:143123600-143124600	Weak transcription	Brain Angular Gyrus	brain
39	chr6:143123600-143124800	Weak transcription	Psoas Muscle	Psoas
40	chr6:143123600-143124800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:143123600-143126200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:143123600-143126800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:143123600-143129400	Weak transcription	HSMMtube	muscle
44	chr6:143123600-143130200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:143123600-143132000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:143123600-143132000	Weak transcription	Fetal Brain Male	brain
47	chr6:143123600-143132200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:143123600-143139400	Weak transcription	Fetal Intestine Small	intestine
49	chr6:143123800-143124800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:143123800-143124800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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