Variant report

Variant	rs2659513
Chromosome Location	chr4:102114349-102114350
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	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021965	0.85[ASN][1000 genomes]
rs1157038	0.90[CEU][hapmap]
rs1354785	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395476	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1506799	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506802	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506803	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506804	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs1543856	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030851	0.81[ASN][1000 genomes]
rs2135609	0.90[CEU][hapmap]
rs2135610	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2135612	0.89[CEU][hapmap]
rs2135614	0.80[ASN][1000 genomes]
rs2174683	0.80[ASN][1000 genomes]
rs2659503	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2659504	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2659505	0.85[CEU][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2659506	0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659508	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]
rs2659509	0.81[CEU][hapmap];0.81[CHB][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659511	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659522	0.89[CEU][hapmap]
rs2659525	0.90[CEU][hapmap]
rs2659530	0.90[CEU][hapmap]
rs2659531	0.89[CEU][hapmap]
rs2659532	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659533	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659534	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659537	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659538	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659539	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659540	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659542	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850347	0.80[CEU][hapmap]
rs2850365	0.80[CEU][hapmap]
rs2850951	0.80[CEU][hapmap]
rs2850980	0.85[ASN][1000 genomes]
rs2850981	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2850982	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2850985	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850990	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850998	0.90[CEU][hapmap]
rs2851003	0.90[CEU][hapmap]
rs3804366	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478191	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs73833252	0.83[ASN][1000 genomes]
rs931871	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs970071	0.90[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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:102102200-102116400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:102104200-102116200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
7	chr4:102104400-102119600	Weak transcription	Ovary	ovary
8	chr4:102104600-102116400	Weak transcription	Dnd41	blood
9	chr4:102105400-102117800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:102106200-102117600	Weak transcription	Gastric	stomach
12	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:102109600-102118000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:102109600-102119400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:102110000-102116600	Weak transcription	NHEK	skin
19	chr4:102110000-102118000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:102111800-102119600	Weak transcription	Fetal Brain Female	brain
22	chr4:102112000-102114400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:102112400-102115000	Enhancers	HepG2	liver
24	chr4:102112800-102116400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:102112800-102117800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:102113000-102116600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:102113000-102117200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:102113000-102118200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:102113200-102116600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:102113200-102117000	Weak transcription	Placenta	Placenta
31	chr4:102113200-102117200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:102113200-102118600	Weak transcription	Lung	lung
33	chr4:102113200-102119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:102113200-102119800	Weak transcription	Fetal Brain Male	brain
35	chr4:102113200-102121000	Weak transcription	HSMM	muscle
36	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
37	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
38	chr4:102113400-102114600	Enhancers	Colon Smooth Muscle	Colon
39	chr4:102113400-102120400	Weak transcription	Fetal Heart	heart
40	chr4:102113400-102120800	Weak transcription	NH-A	brain
41	chr4:102113600-102119400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:102113600-102119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:102113600-102119600	Weak transcription	Brain Angular Gyrus	brain
44	chr4:102113600-102120600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:102113600-102120800	Weak transcription	Right Ventricle	heart
46	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:102113800-102114600	Weak transcription	Osteobl	bone
49	chr4:102113800-102116200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:102113800-102116400	Weak transcription	NHLF	lung

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