Variant report

Variant	rs12565109
Chromosome Location	chr1:227965431-227965432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227960240..227967392-chr1:227972741..227977657,8	K562	blood:
2	chr1:227963946..227966853-chr1:227977108..227980456,3	MCF-7	breast:
3	chr1:227962393..227964421-chr1:227964813..227967727,3	MCF-7	breast:
4	chr1:227963179..227967609-chr1:227968212..227971433,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12563117	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12564736	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564917	1.00[EUR][1000 genomes]
rs12564929	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12565099	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12565618	1.00[EUR][1000 genomes]
rs12565653	1.00[EUR][1000 genomes]
rs12566390	1.00[EUR][1000 genomes]
rs12566716	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12566948	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12567084	1.00[EUR][1000 genomes]
rs12567160	1.00[EUR][1000 genomes]
rs12567934	1.00[EUR][1000 genomes]
rs12568707	1.00[EUR][1000 genomes]
rs1323021	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs13373816	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16841323	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs16847987	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes]
rs16848160	1.00[EUR][1000 genomes]
rs2101862	1.00[EUR][1000 genomes]
rs2313220	1.00[EUR][1000 genomes]
rs34984248	1.00[EUR][1000 genomes]
rs35703429	1.00[EUR][1000 genomes]
rs41305134	0.82[ASN][1000 genomes]
rs4462138	1.00[EUR][1000 genomes]
rs60156730	0.82[ASN][1000 genomes]
rs6665512	1.00[EUR][1000 genomes]
rs6684706	0.82[ASN][1000 genomes]
rs73091000	1.00[EUR][1000 genomes]
rs73092607	1.00[EUR][1000 genomes]
rs73092610	1.00[EUR][1000 genomes]
rs996226	1.00[CHB][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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	9 gene(s)	inside rSNPs	diseases
11	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
2	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
3	chr1:227951800-227970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:227954400-227974600	Weak transcription	HMEC	breast
5	chr1:227955600-227973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227955600-227974000	Weak transcription	Fetal Brain Male	brain
7	chr1:227955800-227972400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227955800-227974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:227955800-227975200	Weak transcription	Hela-S3	cervix
10	chr1:227956000-227974600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:227956200-227968000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:227956600-227973000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:227957000-227966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:227957000-227968200	Weak transcription	Aorta	Aorta
15	chr1:227957000-227970000	Weak transcription	K562	blood
16	chr1:227957000-227970400	Strong transcription	Fetal Intestine Small	intestine
17	chr1:227957600-227972800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:227957800-227967200	Weak transcription	NHEK	skin
19	chr1:227957800-227974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:227958000-227975200	Weak transcription	A549	lung
21	chr1:227958600-227967200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:227961200-227969200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:227961400-227967400	Strong transcription	Spleen	Spleen
24	chr1:227961400-227967800	Enhancers	HSMMtube	muscle
25	chr1:227961800-227966800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:227961800-227967800	Enhancers	NH-A	brain
27	chr1:227962000-227974200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:227962400-227973400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:227962400-227974200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:227962600-227970000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:227962600-227973400	Weak transcription	Primary B cells from cord blood	blood
32	chr1:227962800-227970400	Strong transcription	Thymus	Thymus
33	chr1:227962800-227974000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:227963200-227965800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:227963200-227966600	Strong transcription	Colonic Mucosa	Colon
36	chr1:227963200-227970400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:227963400-227968000	Genic enhancers	Fetal Muscle Leg	muscle
38	chr1:227963400-227970400	Strong transcription	Primary T cells from cord blood	blood
39	chr1:227963400-227970400	Strong transcription	Pancreas	Pancrea
40	chr1:227963600-227966400	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr1:227963600-227970400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:227963800-227966200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:227963800-227966400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:227963800-227974000	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:227964000-227965600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:227964000-227965800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:227964000-227968000	Enhancers	HSMM	muscle
48	chr1:227964000-227973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227964200-227965800	Strong transcription	Fetal Lung	lung
50	chr1:227964200-227966600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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