Variant report

Variant	rs17007107
Chromosome Location	chr1:220271542-220271543
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	chr1:220267849..220270969-chr1:220271218..220274109,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1039206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032738	1.00[YRI][hapmap]
rs12037712	1.00[YRI][hapmap]
rs1557130	1.00[CEU][hapmap]
rs17007135	0.83[YRI][hapmap]
rs17007139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34406824	1.00[JPT][hapmap]
rs3767656	0.86[AMR][1000 genomes]
rs3820455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41274792	0.92[ASN][1000 genomes]
rs57463200	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs58256586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58966246	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73096563	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73096575	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73096577	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73096595	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73098512	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73098518	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73098527	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73098528	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73098530	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73098537	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs874331	1.00[YRI][hapmap]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268200-220275400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:220268400-220273200	Weak transcription	NH-A	brain
3	chr1:220268400-220274800	Weak transcription	Psoas Muscle	Psoas
4	chr1:220268400-220277400	Weak transcription	Aorta	Aorta
5	chr1:220268400-220280400	Weak transcription	Fetal Kidney	kidney
6	chr1:220268400-220283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:220268400-220287400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
9	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:220268600-220274800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:220268600-220274800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:220268600-220274800	Weak transcription	Right Ventricle	heart
13	chr1:220268600-220274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:220268600-220282600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:220268800-220277400	Weak transcription	Colonic Mucosa	Colon
17	chr1:220269000-220272800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:220269000-220275600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:220269200-220271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:220269200-220271600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:220269200-220273200	Weak transcription	Fetal Lung	lung
22	chr1:220269200-220273600	Strong transcription	K562	blood
23	chr1:220269200-220274000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:220269200-220274600	Weak transcription	Left Ventricle	heart
25	chr1:220269200-220274800	Weak transcription	Ovary	ovary
26	chr1:220269200-220275200	Weak transcription	Brain Substantia Nigra	brain
27	chr1:220269200-220275200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:220269200-220275600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:220269200-220276800	Weak transcription	HSMMtube	muscle
30	chr1:220269200-220277400	Weak transcription	Pancreas	Pancrea
31	chr1:220269200-220277600	Weak transcription	Small Intestine	intestine
32	chr1:220269200-220277600	Weak transcription	Thymus	Thymus
33	chr1:220269200-220277800	Weak transcription	Fetal Brain Male	brain
34	chr1:220269200-220279400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:220269200-220279800	Weak transcription	Gastric	stomach
36	chr1:220269200-220280800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:220269200-220282400	Weak transcription	Spleen	Spleen
38	chr1:220269200-220282600	Weak transcription	Esophagus	oesophagus
39	chr1:220269200-220285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:220269200-220291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:220269200-220291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:220269200-220292800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:220269400-220271600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:220269400-220271600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:220269400-220272000	Strong transcription	GM12878-XiMat	blood
47	chr1:220269400-220272200	Weak transcription	Brain Anterior Caudate	brain
48	chr1:220269400-220274000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:220269400-220275400	Weak transcription	Primary T cells from cord blood	blood
50	chr1:220269400-220277000	Weak transcription	Colon Smooth Muscle	Colon

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