Variant report

Variant	rs2659509
Chromosome Location	chr4:102113024-102113025
allele	A/C
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: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1354785	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1395475	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1395476	0.80[JPT][hapmap]
rs1506799	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1506800	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506802	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506803	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506804	0.81[CHB][hapmap];0.82[GIH][hapmap]
rs1543856	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2174683	0.82[GIH][hapmap]
rs2659504	0.82[GIH][hapmap]
rs2659506	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659508	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	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659512	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659513	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]
rs2659532	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659533	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659534	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659537	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659538	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659539	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659540	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659541	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659542	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850982	0.82[GIH][hapmap]
rs2850985	0.91[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850987	0.81[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850989	0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850990	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850991	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850994	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850995	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3804366	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478191	0.81[CHB][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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:102102200-102116400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:102104200-102116200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
8	chr4:102104400-102119600	Weak transcription	Ovary	ovary
9	chr4:102104600-102114000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:102104600-102116400	Weak transcription	Dnd41	blood
11	chr4:102105400-102117800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:102106200-102117600	Weak transcription	Gastric	stomach
14	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:102108000-102113600	Enhancers	Brain Angular Gyrus	brain
17	chr4:102108800-102114200	Weak transcription	Primary B cells from cord blood	blood
18	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:102109600-102118000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:102109600-102119400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:102110000-102116600	Weak transcription	NHEK	skin
23	chr4:102110000-102118000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:102110600-102113600	Enhancers	Rectal Smooth Muscle	rectum
25	chr4:102110600-102114000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:102111200-102113800	Enhancers	Brain Hippocampus Middle	brain
27	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:102111400-102113400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr4:102111400-102113800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:102111600-102114200	Enhancers	Liver	Liver
31	chr4:102111800-102113800	Enhancers	Brain Germinal Matrix	brain
32	chr4:102111800-102119600	Weak transcription	Fetal Brain Female	brain
33	chr4:102112000-102113600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:102112000-102113600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:102112000-102113600	Enhancers	Brain Cingulate Gyrus	brain
36	chr4:102112000-102113800	Enhancers	Brain Substantia Nigra	brain
37	chr4:102112000-102114000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:102112000-102114000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:102112000-102114000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:102112000-102114000	Enhancers	Fetal Intestine Large	intestine
41	chr4:102112000-102114400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr4:102112200-102113200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:102112200-102113200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr4:102112200-102113200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:102112200-102113200	Enhancers	Aorta	Aorta
46	chr4:102112200-102113400	Enhancers	Fetal Heart	heart
47	chr4:102112200-102113600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:102112200-102113800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr4:102112200-102113800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:102112200-102113800	Enhancers	Fetal Muscle Leg	muscle

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