Variant report

Variant	rs12040506
Chromosome Location	chr1:228412392-228412393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228412002..228414034-chr1:228460124..228463067,2	K562	blood:
2	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:
3	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:

Variant related genes	Relation type
ENSG00000269890	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10916296	0.83[ASN][1000 genomes]
rs12022027	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12022323	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12023522	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12023551	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12024329	1.00[AFR][1000 genomes]
rs12024368	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12025837	1.00[AFR][1000 genomes]
rs12026579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12028729	1.00[AFR][1000 genomes]
rs12028894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12029540	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12029981	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12030528	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12031017	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12031390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12031747	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12032850	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12032905	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12033588	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12033624	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12034508	1.00[AFR][1000 genomes]
rs12036437	1.00[AFR][1000 genomes]
rs12036485	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12037417	1.00[AFR][1000 genomes]
rs12037423	1.00[AFR][1000 genomes]
rs12037964	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12038090	0.85[AMR][1000 genomes]
rs12038612	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12039528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040123	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12040394	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12041411	1.00[AFR][1000 genomes]
rs12042084	1.00[AFR][1000 genomes]
rs12043464	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12044918	1.00[AFR][1000 genomes]
rs12044962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12048283	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12049152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12049530	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12120597	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2291999	1.00[AFR][1000 genomes]
rs2298013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28603121	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3754358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3754359	0.92[AMR][1000 genomes]
rs55760713	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55946300	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56154605	0.85[AMR][1000 genomes]
rs56384735	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs74140905	0.92[AMR][1000 genomes]
rs74140962	0.92[AMR][1000 genomes]
rs74140968	0.92[AMR][1000 genomes]
rs74140985	0.92[AMR][1000 genomes]
rs74143629	0.92[AMR][1000 genomes]
rs74143633	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer 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	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228401400-228412600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:228402000-228412600	Weak transcription	Fetal Kidney	kidney
3	chr1:228402200-228412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:228402200-228412600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:228402400-228412400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:228402400-228412600	Weak transcription	HMEC	breast
10	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
11	chr1:228402800-228412600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:228404200-228412600	Weak transcription	Fetal Brain Male	brain
16	chr1:228408600-228412400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:228410000-228416600	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr1:228410200-228413600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:228410200-228414800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr1:228410400-228412400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:228410400-228412600	Strong transcription	Fetal Lung	lung
22	chr1:228410400-228412800	ZNF genes & repeats	Aorta	Aorta
23	chr1:228410400-228415600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:228410600-228416400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:228410800-228413000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr1:228410800-228416800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:228411000-228413200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr1:228411000-228415000	Weak transcription	Small Intestine	intestine
29	chr1:228411400-228413400	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr1:228411400-228413600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:228411600-228413200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr1:228411600-228413600	ZNF genes & repeats	Fetal Stomach	stomach
33	chr1:228411600-228413800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:228411600-228413800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:228411600-228416000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:228411600-228416800	Strong transcription	Dnd41	blood
37	chr1:228411800-228412800	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr1:228411800-228412800	ZNF genes & repeats	Fetal Thymus	thymus
39	chr1:228411800-228413000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:228411800-228413000	ZNF genes & repeats	Gastric	stomach
41	chr1:228411800-228413200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:228411800-228413200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr1:228411800-228413200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr1:228411800-228413200	ZNF genes & repeats	Esophagus	oesophagus
45	chr1:228411800-228413200	ZNF genes & repeats	Ovary	ovary
46	chr1:228411800-228413400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr1:228411800-228413400	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr1:228411800-228413600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:228411800-228413600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:228411800-228413800	ZNF genes & repeats	Pancreas	Pancrea

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