Variant report

Variant	rs258962
Chromosome Location	chr7:87007179-87007180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86946860..86949109-chr7:87005374..87008046,2	MCF-7	breast:
2	chr7:87006049..87008428-chr7:87014986..87016616,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10247098	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs1089472	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373593	0.90[CEU][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs258963	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs258964	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258965	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31627	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31629	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31630	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31632	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31634	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31635	0.89[CEU][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31640	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31644	0.90[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31645	0.90[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31649	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs31651	1.00[ASW][hapmap];0.90[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs31652	0.83[LWK][hapmap];0.98[MKK][hapmap]
rs31653	0.90[CEU][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs31658	0.90[CEU][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs31659	0.90[CEU][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs31660	0.90[CEU][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs31662	0.90[CEU][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs3789250	0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs39606	0.91[ASW][hapmap];0.90[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs6949638	0.94[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs6966140	0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs701339	0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7802658	0.81[CHB][hapmap]
rs802042	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs802054	0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs802055	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs802057	0.82[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802062	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1029486	chr7:86856387-87121976	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv539004	chr7:86856387-87121976	Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1814401	chr7:86857553-87034167	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	esv1826474	chr7:86857553-87034167	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv428177	chr7:86857553-87034167	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv1024376	chr7:86905796-87129346	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	nsv888678	chr7:86932085-87101407	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86975600-87025800	Weak transcription	Gastric	stomach
2	chr7:86975600-87029800	Weak transcription	Psoas Muscle	Psoas
3	chr7:86975800-87031000	Weak transcription	Pancreas	Pancrea
4	chr7:86976800-87016000	Weak transcription	Aorta	Aorta
5	chr7:86979400-87024600	Weak transcription	Small Intestine	intestine
6	chr7:86980000-87085600	Weak transcription	Right Ventricle	heart
7	chr7:86980200-87011800	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:86980200-87020400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:86980200-87028600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:86982400-87027600	Weak transcription	HSMMtube	muscle
11	chr7:86983600-87027000	Weak transcription	Colonic Mucosa	Colon
12	chr7:86983800-87016000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:86983800-87027800	Weak transcription	Brain Substantia Nigra	brain
14	chr7:86984000-87011600	Weak transcription	Brain Anterior Caudate	brain
15	chr7:86984800-87027000	Weak transcription	Thymus	Thymus
16	chr7:86985200-87011600	Weak transcription	GM12878-XiMat	blood
17	chr7:86985200-87015800	Weak transcription	Fetal Kidney	kidney
18	chr7:86985200-87027000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:86985400-87018000	Weak transcription	Brain Germinal Matrix	brain
20	chr7:86985400-87027600	Weak transcription	NHLF	lung
21	chr7:86985600-87011000	Weak transcription	Placenta	Placenta
22	chr7:86985600-87017000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:86985600-87017000	Weak transcription	Fetal Thymus	thymus
24	chr7:86985600-87026200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:86986000-87011600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:86986600-87011600	Weak transcription	Ovary	ovary
27	chr7:86987000-87007600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:86987000-87015800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr7:86987000-87016000	Weak transcription	Fetal Stomach	stomach
30	chr7:86987000-87016000	Weak transcription	Lung	lung
31	chr7:86987000-87024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:86987000-87028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:86987000-87051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:86987200-87016000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:86987400-87022200	Weak transcription	Brain Angular Gyrus	brain
36	chr7:86987400-87022800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:86987400-87024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:86987400-87027800	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:86987400-87028400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:86987600-87007800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:86987600-87024400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr7:86988400-87028000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr7:86988600-87014000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:86989000-87027600	Weak transcription	NH-A	brain
45	chr7:86989000-87027600	Weak transcription	Osteobl	bone
46	chr7:86989400-87022200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:86989400-87027800	Weak transcription	HSMM	muscle
48	chr7:86989600-87011600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:86991600-87015800	Weak transcription	Dnd41	blood
50	chr7:86992000-87016000	Weak transcription	Esophagus	oesophagus

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