Variant report

Variant	rs12077565
Chromosome Location	chr1:226041301-226041302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226041094-226041414	K562	blood:	n/a	n/a
2	POLR2A	chr1:226040494-226041566	A549	lung:	n/a	n/a
3	POLR2A	chr1:226040229-226042167	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226038307..226042475-chr1:226101136..226103388,3	K562	blood:
2	chr1:226039534..226042105-chr1:226096713..226099428,2	MCF-7	breast:
3	chr1:226038828..226041322-chr1:226049497..226051238,2	K562	blood:

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000243709	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10915883	0.98[AFR][1000 genomes]
rs10915886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915887	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915890	0.82[AFR][1000 genomes]
rs12070110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071072	0.82[AFR][1000 genomes]
rs12071104	0.82[AFR][1000 genomes]
rs12071413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075664	0.97[AFR][1000 genomes]
rs12077174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079891	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082207	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083928	1.00[AFR][1000 genomes]
rs12084714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097377	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2292561	0.88[AFR][1000 genomes]
rs35273824	0.81[AFR][1000 genomes]
rs35684337	0.81[AFR][1000 genomes]
rs55706532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56112955	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56325807	0.90[AFR][1000 genomes]
rs58852301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59728172	0.90[AFR][1000 genomes]
rs60132040	0.89[AFR][1000 genomes]
rs60739570	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61304305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150526	0.86[AFR][1000 genomes]
rs74150531	0.87[AMR][1000 genomes]
rs74150536	0.90[AFR][1000 genomes]
rs74150537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150539	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
3	chr1:226016000-226051000	Weak transcription	NH-A	brain
4	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
5	chr1:226020600-226042000	Weak transcription	Hela-S3	cervix
6	chr1:226020600-226042400	Weak transcription	HSMM	muscle
7	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
9	chr1:226030400-226046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
11	chr1:226033600-226041600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr1:226033600-226053000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr1:226034000-226056800	Strong transcription	Adipose Nuclei	Adipose
15	chr1:226034000-226063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:226034200-226062800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:226034600-226047600	Weak transcription	NHEK	skin
18	chr1:226036000-226049000	Weak transcription	A549	lung
19	chr1:226036400-226043200	Strong transcription	Fetal Intestine Large	intestine
20	chr1:226036600-226041800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:226036600-226042600	Strong transcription	Colonic Mucosa	Colon
22	chr1:226036600-226064600	Weak transcription	Fetal Heart	heart
23	chr1:226036800-226044800	Genic enhancers	Fetal Thymus	thymus
24	chr1:226036800-226048600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:226036800-226058600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
27	chr1:226037000-226045400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:226037000-226054200	Weak transcription	Small Intestine	intestine
29	chr1:226037400-226041400	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr1:226037400-226048600	Weak transcription	Dnd41	blood
31	chr1:226037400-226051800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:226037600-226043400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:226037600-226051800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:226037600-226060600	Strong transcription	Placenta	Placenta
35	chr1:226037800-226042800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:226037800-226043200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:226037800-226045000	Strong transcription	Gastric	stomach
38	chr1:226037800-226046200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:226037800-226048400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:226037800-226065200	Weak transcription	Right Atrium	heart
41	chr1:226038000-226052400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:226038200-226041400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:226038200-226042800	Strong transcription	Spleen	Spleen
44	chr1:226038200-226043000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:226038200-226043200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:226038200-226043400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:226038400-226041400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:226038400-226042000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:226038400-226042000	Strong transcription	Brain Hippocampus Middle	brain
50	chr1:226038400-226059600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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