Variant report

Variant	rs61812596
Chromosome Location	chr1:154414691-154414692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154401786..154404532-chr1:154413417..154415203,2	K562	blood:
2	chr1:154413948..154418058-chr1:154421616..154424516,3	MCF-7	breast:
3	chr1:154377274..154378530-chr1:154414662..154415293,4	MCF-7	breast:
4	chr1:154414588..154416546-chr1:154448223..154449736,2	K562	blood:
5	chr1:154406170..154408032-chr1:154413568..154416064,2	MCF-7	breast:
6	chr1:154410246..154412652-chr1:154413063..154415706,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10159236	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265618	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11804305	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12023358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047973	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048091	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048950	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4308966	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4329505	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4345796	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845626	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55800510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57502626	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812592	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812593	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812594	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812599	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61812626	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
3	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
5	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:154407400-154416200	Genic enhancers	Liver	Liver
7	chr1:154407400-154417400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:154407600-154417200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:154407600-154418600	Weak transcription	Ovary	ovary
10	chr1:154408600-154414800	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:154408800-154416000	Weak transcription	Right Ventricle	heart
14	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:154409200-154417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:154409200-154420600	Weak transcription	Gastric	stomach
20	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
21	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
22	chr1:154410400-154418000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:154410600-154415800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:154410800-154418600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:154410800-154418800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:154411000-154415600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:154411400-154416000	Weak transcription	Left Ventricle	heart
28	chr1:154411600-154415400	Weak transcription	Colonic Mucosa	Colon
29	chr1:154412400-154415800	Enhancers	Fetal Thymus	thymus
30	chr1:154412600-154415600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
32	chr1:154412800-154414800	Enhancers	GM12878-XiMat	blood
33	chr1:154412800-154415600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:154412800-154417000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:154412800-154425800	Weak transcription	HepG2	liver
36	chr1:154413000-154419600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:154413200-154415000	Enhancers	Esophagus	oesophagus
38	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:154413400-154415000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr1:154413400-154415000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:154413400-154415200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:154413400-154415800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:154413400-154417800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:154413600-154414800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr1:154413600-154414800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:154413600-154415000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:154413600-154415800	Enhancers	HMEC	breast
48	chr1:154413600-154418800	Genic enhancers	Colon Smooth Muscle	Colon
49	chr1:154413600-154419600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:154413800-154415000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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