Variant report

Variant	rs9390652
Chromosome Location	chr6:149337489-149337490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149335195..149337795-chr6:149343011..149345785,3	MCF-7	breast:
2	chr6:149335068..149337695-chr6:149751708..149753851,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10457075	0.84[CEU][hapmap]
rs10457839	0.83[CEU][hapmap]
rs12153925	0.82[CEU][hapmap]
rs12191733	0.86[JPT][hapmap]
rs12193145	0.86[AMR][1000 genomes]
rs12197040	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs12200909	0.87[CEU][hapmap]
rs12202158	0.83[CEU][hapmap]
rs12206419	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs12214448	0.92[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13217006	0.83[CEU][hapmap]
rs17669546	0.88[CEU][hapmap]
rs1890610	0.82[GIH][hapmap]
rs1934221	0.88[CEU][hapmap]
rs1934222	0.83[CEU][hapmap]
rs1934227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153252	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs2185250	0.82[GIH][hapmap]
rs34368036	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3949414	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs4335010	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4336467	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs6570921	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570923	0.84[CEU][hapmap]
rs6570924	0.84[CEU][hapmap]
rs6570926	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs6570927	0.84[CEU][hapmap]
rs6570932	0.82[GIH][hapmap]
rs6914281	0.84[CEU][hapmap]
rs6914318	0.85[GIH][hapmap]
rs6914925	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs6917010	0.85[GIH][hapmap]
rs6930713	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs6930963	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7762928	0.83[GIH][hapmap]
rs7770997	0.83[AMR][1000 genomes]
rs9322165	0.83[CEU][hapmap]
rs9390648	0.81[CEU][hapmap]
rs9390649	0.88[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9390650	0.81[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs9485353	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs9498199	0.87[CEU][hapmap]
rs9498201	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs9498202	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs9498204	0.85[GIH][hapmap]

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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149320200-149344800	Weak transcription	Left Ventricle	heart
3	chr6:149321600-149340600	Weak transcription	Aorta	Aorta
4	chr6:149321800-149340200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:149323000-149342600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:149327200-149340200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:149327200-149340600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:149327600-149342200	Weak transcription	Dnd41	blood
11	chr6:149329400-149340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:149329800-149340200	Weak transcription	Ovary	ovary
13	chr6:149332600-149337800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:149333000-149337600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:149333000-149337600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:149333400-149340800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:149333600-149340400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:149333800-149341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:149333800-149341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:149333800-149342200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
22	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
23	chr6:149334600-149337600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:149335000-149337600	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:149335200-149337600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr6:149335200-149337600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:149335200-149337600	Enhancers	NH-A	brain
28	chr6:149335200-149337800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:149335200-149338000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:149335200-149338200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:149335200-149338200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:149335200-149338200	Enhancers	Fetal Muscle Leg	muscle
33	chr6:149335400-149337600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:149335600-149337600	Enhancers	Osteobl	bone
35	chr6:149336000-149345200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:149336200-149337600	Enhancers	NHLF	lung
37	chr6:149336200-149342800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:149336200-149344200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:149336200-149344400	Weak transcription	Fetal Intestine Small	intestine
40	chr6:149336200-149345200	Weak transcription	Right Atrium	heart
41	chr6:149336200-149349800	Weak transcription	Brain Anterior Caudate	brain
42	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
43	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
44	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
45	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:149336400-149338200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:149336400-149341000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:149336400-149347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:149336600-149347400	Weak transcription	Adipose Nuclei	Adipose

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