Variant report

Variant	rs2128646
Chromosome Location	chr1:92564147-92564148
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92556197..92558083-chr1:92563000..92565811,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1014415	1.00[JPT][hapmap]
rs10159094	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1023041	1.00[JPT][hapmap]
rs10875204	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs10875209	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875214	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875319	1.00[JPT][hapmap]
rs11165984	1.00[JPT][hapmap]
rs11166042	1.00[JPT][hapmap]
rs11166141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs11166144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1157469	0.91[CEU][hapmap]
rs1157470	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11577572	1.00[JPT][hapmap]
rs11588153	1.00[JPT][hapmap]
rs12119246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1226183	1.00[JPT][hapmap]
rs1226187	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12404806	1.00[JPT][hapmap]
rs12729867	1.00[JPT][hapmap]
rs1483022	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1487540	1.00[JPT][hapmap]
rs1872007	1.00[JPT][hapmap]
rs1982720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2046620	1.00[JPT][hapmap]
rs2087194	1.00[JPT][hapmap]
rs2093879	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2128645	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2391114	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839877	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2893200	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3103176	1.00[JPT][hapmap]
rs3103178	1.00[JPT][hapmap]
rs3103181	1.00[JPT][hapmap]
rs3131814	1.00[JPT][hapmap]
rs3131828	1.00[JPT][hapmap]
rs3851271	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3851272	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3851273	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4437922	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4623754	1.00[CHB][hapmap]
rs4658128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658289	1.00[CHB][hapmap]
rs4658290	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658294	1.00[JPT][hapmap]
rs4658298	1.00[JPT][hapmap]
rs4658299	1.00[JPT][hapmap]
rs488849	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs490800	1.00[JPT][hapmap]
rs492164	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs493595	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs504606	1.00[JPT][hapmap]
rs506375	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs507452	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs511546	1.00[JPT][hapmap]
rs515280	1.00[JPT][hapmap]
rs519932	1.00[JPT][hapmap]
rs527412	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs529135	1.00[JPT][hapmap]
rs534547	1.00[JPT][hapmap]
rs547699	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs551909	0.86[CEU][hapmap]
rs553861	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs556980	1.00[JPT][hapmap]
rs563113	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs563606	1.00[JPT][hapmap]
rs569593	1.00[JPT][hapmap]
rs570368	1.00[JPT][hapmap]
rs573044	1.00[JPT][hapmap]
rs575805	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6604080	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6604082	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs6684317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6699855	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7533077	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7541482	0.86[CEU][hapmap]
rs7542358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7542373	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7545076	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs981583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription 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	19 gene(s)	inside rSNPs	diseases
6	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
19	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv871415	chr1:92340684-92641607	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	esv2750842	chr1:92356781-92579675	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv871144	chr1:92380302-92641607	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	nsv1008863	chr1:92441031-92567045	Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
25	nsv535032	chr1:92441031-92567045	ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
26	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
27	nsv1009079	chr1:92525630-92595669	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
28	nsv546821	chr1:92525678-92650349	ZNF genes & repeats Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
29	esv1918863	chr1:92564147-92564148	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92552000-92577400	Weak transcription	Fetal Brain Male	brain
2	chr1:92552200-92580400	Weak transcription	Aorta	Aorta
3	chr1:92552200-92583800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:92552400-92567000	Weak transcription	Fetal Stomach	stomach
5	chr1:92552400-92586000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:92552400-92595200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:92552600-92566800	Weak transcription	Adipose Nuclei	Adipose
8	chr1:92552600-92568200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:92552600-92568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:92552600-92568800	Weak transcription	Fetal Lung	lung
11	chr1:92552600-92568800	Weak transcription	Placenta	Placenta
12	chr1:92552600-92568800	Weak transcription	Dnd41	blood
13	chr1:92552600-92579200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:92552600-92582400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:92552600-92590000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:92552600-92591600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:92552600-92613400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:92552800-92569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:92552800-92579000	Weak transcription	Psoas Muscle	Psoas
20	chr1:92552800-92613600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:92553000-92570000	Weak transcription	Fetal Intestine Large	intestine
22	chr1:92553200-92576600	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:92553800-92575800	Weak transcription	Fetal Kidney	kidney
24	chr1:92554400-92583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:92555200-92580400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:92555200-92620400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:92555400-92573400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:92555400-92580400	Weak transcription	Ovary	ovary
29	chr1:92555800-92568800	Weak transcription	Brain Germinal Matrix	brain
30	chr1:92555800-92576000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:92556000-92613600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:92556600-92613400	Weak transcription	Fetal Brain Female	brain
33	chr1:92557000-92571800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:92557400-92598000	Weak transcription	Spleen	Spleen
35	chr1:92558000-92583000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:92558000-92604000	Weak transcription	Left Ventricle	heart
37	chr1:92558800-92568200	Weak transcription	Liver	Liver
38	chr1:92560000-92613600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:92560400-92580400	Weak transcription	Lung	lung
40	chr1:92560600-92573600	Weak transcription	Right Ventricle	heart
41	chr1:92560600-92590800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:92561000-92573600	Weak transcription	Fetal Heart	heart
43	chr1:92561200-92619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:92561600-92568400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:92561600-92590000	Weak transcription	Brain Substantia Nigra	brain
46	chr1:92562000-92571000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:92562200-92568800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:92562600-92565400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:92562600-92569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:92562600-92582800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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