Variant report

Variant	rs2489180
Chromosome Location	chr1:92270519-92270520
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	chr1:92245858..92248144-chr1:92269665..92271280,2	K562	blood:
2	chr1:92269279..92272009-chr1:92273334..92276001,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10747477	1.00[AMR][1000 genomes]
rs1892006	1.00[AMR][1000 genomes]
rs2450929	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2450930	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2479869	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2479873	1.00[AMR][1000 genomes]
rs2479874	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2479877	1.00[AMR][1000 genomes]
rs2480707	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2489172	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2489177	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2489181	1.00[AMR][1000 genomes]
rs2489191	1.00[AMR][1000 genomes]
rs2492088	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2492089	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2492090	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2634035	1.00[AMR][1000 genomes]
rs2634037	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2634039	1.00[AMR][1000 genomes]
rs2770184	1.00[YRI][hapmap]
rs2770190	1.00[AMR][1000 genomes]
rs2799513	1.00[AMR][1000 genomes]
rs2799529	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2799530	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2799531	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2799534	1.00[AMR][1000 genomes]
rs2799538	1.00[AMR][1000 genomes]
rs2810892	1.00[AMR][1000 genomes]
rs2987446	1.00[AMR][1000 genomes]
rs2987447	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2996475	1.00[AMR][1000 genomes]
rs2996483	1.00[AMR][1000 genomes]
rs57426601	1.00[AMR][1000 genomes]
rs66702902	1.00[AMR][1000 genomes]
rs6677910	1.00[AMR][1000 genomes]
rs6703194	1.00[AMR][1000 genomes]
rs7527065	1.00[AMR][1000 genomes]
rs7531181	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92257600-92279400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:92258400-92271400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:92258800-92272400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:92260400-92271200	Strong transcription	HepG2	liver
5	chr1:92262800-92277000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:92264600-92271800	Weak transcription	Aorta	Aorta
7	chr1:92264800-92284200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:92265200-92271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:92266800-92277400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:92267800-92273400	Enhancers	Adipose Nuclei	Adipose
11	chr1:92268200-92270600	Enhancers	Esophagus	oesophagus
12	chr1:92268200-92274600	Enhancers	Placenta	Placenta
13	chr1:92268400-92270600	Enhancers	Right Atrium	heart
14	chr1:92268400-92272800	Enhancers	Fetal Thymus	thymus
15	chr1:92268400-92273400	Enhancers	Fetal Lung	lung
16	chr1:92268400-92273400	Enhancers	Fetal Muscle Leg	muscle
17	chr1:92268400-92273400	Enhancers	Lung	lung
18	chr1:92268600-92270600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:92268600-92270800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:92268600-92271600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:92268600-92272000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:92268600-92273400	Enhancers	Right Ventricle	heart
23	chr1:92268600-92273400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:92268600-92275200	Enhancers	NHDF-Ad	bronchial
25	chr1:92268600-92275800	Enhancers	Pancreas	Pancrea
26	chr1:92268800-92271800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:92268800-92272000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:92268800-92273400	Enhancers	Colon Smooth Muscle	Colon
29	chr1:92268800-92273400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr1:92268800-92273400	Enhancers	NHLF	lung
31	chr1:92269000-92271000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:92269000-92271000	Weak transcription	Psoas Muscle	Psoas
33	chr1:92269000-92273400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:92269200-92270600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr1:92269200-92270600	Enhancers	Colonic Mucosa	Colon
36	chr1:92269200-92271200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:92269200-92272200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:92269200-92273400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:92269200-92273400	Enhancers	Fetal Kidney	kidney
40	chr1:92269400-92270600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:92269400-92270800	Bivalent Enhancer	HMEC	breast
42	chr1:92269400-92271000	Flanking Active TSS	GM12878-XiMat	blood
43	chr1:92269400-92271200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:92269400-92273400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:92269400-92275600	Enhancers	Fetal Heart	heart
46	chr1:92269600-92271200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:92269600-92271200	Enhancers	A549	lung
48	chr1:92269600-92272200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:92269600-92273600	Enhancers	Ovary	ovary
50	chr1:92269600-92275800	Enhancers	Left Ventricle	heart

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