Variant report

Variant	rs2275423
Chromosome Location	chr6:149340390-149340391
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149339358..149341194-chr6:149347879..149350031,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10457074	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1317171	0.86[CEU][hapmap]
rs1934224	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs2340751	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340798	0.87[CEU][hapmap]
rs2340801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2340802	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2500549	0.94[YRI][hapmap]
rs2879843	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4318907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4377808	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897076	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6570920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6904550	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6911303	0.87[JPT][hapmap]
rs6915298	0.86[CEU][hapmap]
rs6930989	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6931675	0.86[CEU][hapmap]
rs6931744	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6936176	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7738162	0.83[CEU][hapmap]
rs7747463	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7748978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765778	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7774457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7774887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776117	0.87[CEU][hapmap]
rs9285516	0.82[CEU][hapmap]
rs9377187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377188	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399678	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][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	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:81 , 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	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:149323000-149342600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:149327200-149340600	Weak transcription	Primary B cells from cord blood	blood
7	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:149327600-149342200	Weak transcription	Dnd41	blood
9	chr6:149329400-149340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:149333400-149340800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:149333600-149340400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:149333800-149341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:149333800-149341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:149333800-149342200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
16	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
17	chr6:149336000-149345200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:149336200-149342800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:149336200-149344200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:149336200-149344400	Weak transcription	Fetal Intestine Small	intestine
21	chr6:149336200-149345200	Weak transcription	Right Atrium	heart
22	chr6:149336200-149349800	Weak transcription	Brain Anterior Caudate	brain
23	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
24	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
25	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
26	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:149336400-149341000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:149336400-149347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:149336600-149347400	Weak transcription	Adipose Nuclei	Adipose
31	chr6:149336800-149340600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:149336800-149341000	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:149336800-149353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:149337200-149340400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:149337200-149340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:149337200-149340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:149337200-149340800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:149337200-149340800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:149337200-149342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:149337200-149342800	Weak transcription	Fetal Lung	lung
41	chr6:149337200-149344800	Weak transcription	Fetal Heart	heart
42	chr6:149337200-149347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:149337200-149353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:149337400-149340400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:149337400-149341000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:149337600-149343600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:149337600-149347200	Weak transcription	Osteobl	bone
48	chr6:149337600-149347400	Weak transcription	NH-A	brain
49	chr6:149337600-149352800	Weak transcription	NHLF	lung
50	chr6:149337600-149353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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