Variant report

Variant	rs2659508
Chromosome Location	chr4:102111169-102111170
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	chr4:102095517..102097376-chr4:102110682..102112984,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1021965	0.86[ASN][1000 genomes]
rs1157038	0.89[CEU][hapmap]
rs1354785	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1395475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1395476	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1506799	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1506800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1506802	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1506803	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1506804	0.89[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1543856	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030851	0.82[ASN][1000 genomes]
rs2135609	0.89[CEU][hapmap]
rs2135610	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2135612	0.89[CEU][hapmap]
rs2135614	0.82[ASN][1000 genomes]
rs2174683	0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[ASN][1000 genomes]
rs2659503	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2659504	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2659505	0.82[CEU][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2659506	1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659509	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659511	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659522	0.88[CEU][hapmap]
rs2659525	0.89[CEU][hapmap]
rs2659530	0.89[CEU][hapmap]
rs2659531	0.88[CEU][hapmap]
rs2659532	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659533	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659534	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659537	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659538	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659539	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659540	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659542	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850980	0.86[ASN][1000 genomes]
rs2850981	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2850982	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2850985	0.90[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850986	0.89[YRI][hapmap]
rs2850987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850990	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850991	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850995	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850998	0.89[CEU][hapmap]
rs2851003	0.89[CEU][hapmap]
rs3804366	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4478191	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs73833252	0.85[ASN][1000 genomes]
rs931871	0.85[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs970071	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102090800-102112200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:102096200-102112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:102096600-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:102096600-102112000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:102096600-102112000	Weak transcription	Right Ventricle	heart
8	chr4:102097400-102112200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:102097800-102112200	Weak transcription	Adipose Nuclei	Adipose
10	chr4:102097800-102112200	Weak transcription	Left Ventricle	heart
11	chr4:102097800-102112600	Weak transcription	Pancreas	Pancrea
12	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:102102000-102112200	Weak transcription	Psoas Muscle	Psoas
14	chr4:102102000-102112800	Weak transcription	Right Atrium	heart
15	chr4:102102200-102112200	Weak transcription	Aorta	Aorta
16	chr4:102102200-102116400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:102104000-102112200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:102104200-102112200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:102104200-102112800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:102104200-102116200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:102104400-102112600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
24	chr4:102104400-102119600	Weak transcription	Ovary	ovary
25	chr4:102104600-102112200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:102104600-102112400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:102104600-102114000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:102104600-102116400	Weak transcription	Dnd41	blood
29	chr4:102105400-102112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:102105400-102113000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:102105400-102117800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:102105600-102112600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:102105600-102112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:102106200-102111400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:102106200-102112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:102106200-102112800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:102106200-102113000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:102106200-102113000	Weak transcription	HMEC	breast
40	chr4:102106200-102117600	Weak transcription	Gastric	stomach
41	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:102106600-102112200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:102106600-102112400	Weak transcription	Fetal Intestine Small	intestine
44	chr4:102107200-102112000	Weak transcription	Fetal Intestine Large	intestine
45	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:102107800-102112800	Enhancers	Brain Anterior Caudate	brain
47	chr4:102108000-102113600	Enhancers	Brain Angular Gyrus	brain
48	chr4:102108200-102112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:102108400-102111200	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:102108400-102112200	Weak transcription	H9 Cell Line	embryonic stem cell

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