Variant report

Variant	rs2659530
Chromosome Location	chr4:102160010-102160011
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	chr4:102152625..102154984-chr4:102158702..102160771,2	MCF-7	breast:
2	chr4:102158963..102160563-chr4:102166791..102168872,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1157038	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1395474	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395475	0.90[CEU][hapmap]
rs1472825	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1506800	0.90[CEU][hapmap]
rs2135608	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2135609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2135612	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659508	0.89[CEU][hapmap]
rs2659511	0.82[CEU][hapmap]
rs2659512	0.90[CEU][hapmap]
rs2659513	0.90[CEU][hapmap]
rs2659516	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659517	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659518	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659519	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659520	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659521	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659522	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659523	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659533	0.89[CEU][hapmap]
rs2659534	0.89[CEU][hapmap]
rs2659538	0.89[CEU][hapmap]
rs2659541	0.90[CEU][hapmap]
rs2850347	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850365	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850373	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850951	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850972	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850985	0.82[CEU][hapmap]
rs2850987	0.90[CEU][hapmap]
rs2850989	1.00[CEU][hapmap]
rs2850994	0.89[CEU][hapmap]
rs2850996	0.88[EUR][1000 genomes]
rs2850998	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850999	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2851001	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2851002	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2851003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851009	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804366	0.89[CEU][hapmap]
rs67445056	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs970071	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102146400-102162000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:102152400-102160200	Weak transcription	Aorta	Aorta
3	chr4:102152800-102165600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:102153000-102165600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:102153000-102165600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:102154000-102160200	Weak transcription	HSMM	muscle
7	chr4:102157400-102160200	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:102157400-102165400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:102157800-102179600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:102158000-102160400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr4:102158400-102161000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:102159000-102160800	Enhancers	Adipose Nuclei	Adipose
13	chr4:102159000-102161000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:102159000-102161000	Enhancers	NHLF	lung
15	chr4:102159000-102161200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:102159200-102160200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:102159200-102162000	Weak transcription	Ovary	ovary
18	chr4:102159200-102162200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:102159200-102163000	Weak transcription	Stomach Mucosa	stomach
20	chr4:102159200-102164000	Weak transcription	Gastric	stomach
21	chr4:102159200-102164000	Weak transcription	Pancreas	Pancrea
22	chr4:102159200-102164000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:102159200-102165600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:102159200-102165600	Weak transcription	Brain Angular Gyrus	brain
25	chr4:102159200-102165600	Weak transcription	Esophagus	oesophagus
26	chr4:102159200-102179800	Weak transcription	Psoas Muscle	Psoas
27	chr4:102159400-102160200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:102159400-102160400	Weak transcription	Spleen	Spleen
29	chr4:102159400-102160600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:102159400-102161000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:102159600-102160400	Enhancers	HMEC	breast
32	chr4:102159600-102160600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:102159600-102161000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:102159600-102161000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:102159600-102161000	Enhancers	Hela-S3	cervix
36	chr4:102159600-102161200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:102159600-102161200	Enhancers	NHDF-Ad	bronchial
38	chr4:102159600-102161200	Enhancers	Osteobl	bone
39	chr4:102159600-102161400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:102159800-102160400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:102159800-102160400	Enhancers	Small Intestine	intestine
42	chr4:102159800-102160400	Flanking Active TSS	A549	lung
43	chr4:102159800-102160400	Enhancers	NH-A	brain
44	chr4:102159800-102160400	Flanking Active TSS	NHEK	skin
45	chr4:102159800-102160600	Enhancers	Primary T cells from cord blood	blood
46	chr4:102159800-102160600	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:102159800-102160600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:102159800-102160600	Enhancers	HUVEC	blood vessel
49	chr4:102159800-102160600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr4:102159800-102160800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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