Variant report

Variant	rs10457842
Chromosome Location	chr6:149415604-149415605
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149401028..149403801-chr6:149413849..149415930,2	MCF-7	breast:
2	chr6:149409974..149412815-chr6:149414835..149416934,2	K562	blood:
3	chr6:149413026..149415707-chr6:149636952..149639609,2	MCF-7	breast:
4	chr6:149411028..149414367-chr6:149415075..149417889,3	MCF-7	breast:
5	chr6:149414073..149415893-chr6:149615671..149617691,2	MCF-7	breast:
6	chr6:149381088..149383058-chr6:149414648..149416261,2	MCF-7	breast:
7	chr6:149350211..149352689-chr6:149414804..149416948,2	MCF-7	breast:
8	chr6:149414327..149416507-chr6:149637915..149640707,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10457075	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10457839	1.00[JPT][hapmap]
rs10499251	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12153925	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12196284	1.00[JPT][hapmap]
rs12197040	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12200909	1.00[JPT][hapmap]
rs12202158	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12206419	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12216011	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1316376	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316534	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1316536	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13191650	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13217006	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17669546	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1890610	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1890612	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1934221	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1934222	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2153251	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2153252	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2185250	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2340800	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3949414	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4336467	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4454159	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6570923	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570924	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570926	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570927	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570932	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6570939	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902195	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902487	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914281	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914318	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914925	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6917010	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6924503	0.85[EUR][1000 genomes]
rs6930713	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6940664	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6940915	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7740618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7762928	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7773409	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7775412	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9485353	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498199	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498201	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498202	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498204	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498205	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9498207	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9498214	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149402400-149416200	Weak transcription	Fetal Heart	heart
2	chr6:149410800-149418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:149411800-149415800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:149413000-149416000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:149413000-149416000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr6:149413000-149416000	Enhancers	Dnd41	blood
7	chr6:149413200-149416000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:149413400-149416000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:149413600-149416000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:149414000-149415800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:149414200-149417600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:149414200-149418400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:149414400-149416200	Enhancers	Fetal Lung	lung
14	chr6:149414400-149416400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:149414400-149416400	Enhancers	NH-A	brain
16	chr6:149414600-149415800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:149414600-149416000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:149414600-149416200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:149414600-149416400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:149414600-149416600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:149414600-149416600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:149414600-149416800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:149414600-149416800	Enhancers	Osteobl	bone
24	chr6:149414600-149417200	Enhancers	Fetal Stomach	stomach
25	chr6:149414600-149417400	Enhancers	Rectal Smooth Muscle	rectum
26	chr6:149414600-149417600	Enhancers	Primary T cells from cord blood	blood
27	chr6:149414800-149416000	Enhancers	Hela-S3	cervix
28	chr6:149414800-149416200	Enhancers	Ovary	ovary
29	chr6:149414800-149416400	Enhancers	Placenta	Placenta
30	chr6:149414800-149418000	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:149415000-149415800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr6:149415000-149416000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:149415000-149416000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:149415000-149416000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:149415000-149416200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:149415000-149416200	Enhancers	Brain Substantia Nigra	brain
37	chr6:149415000-149416600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:149415000-149417400	Enhancers	Fetal Kidney	kidney
39	chr6:149415200-149416200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:149415200-149416600	Enhancers	GM12878-XiMat	blood
41	chr6:149415200-149417200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:149415200-149418200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:149415200-149419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:149415400-149415800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:149415400-149416200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr6:149415400-149416400	Weak transcription	Adipose Nuclei	Adipose
47	chr6:149415400-149416400	Enhancers	Brain Anterior Caudate	brain
48	chr6:149415400-149418400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:149415600-149416000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:149415600-149416000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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