Variant report

Variant	rs12562288
Chromosome Location	chr1:211750362-211750363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211715152..211718143-chr1:211748506..211750792,2	K562	blood:
2	chr1:211749200..211754595-chr1:211816014..211824648,8	K562	blood:
3	chr1:211686187..211688121-chr1:211747912..211750697,2	K562	blood:
4	chr1:211750060..211753695-chr1:211824093..211827463,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222080	Chromatin interaction
ENSG00000228792	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11119772	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11553543	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12091351	1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs17017739	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs17017758	0.91[EUR][1000 genomes]
rs17017761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017782	0.92[JPT][hapmap]
rs17838268	0.97[AFR][1000 genomes]
rs2278652	1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs3738198	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs58859157	0.91[EUR][1000 genomes]
rs61336072	0.96[AFR][1000 genomes]
rs61632665	0.84[AFR][1000 genomes]
rs73075110	0.91[EUR][1000 genomes]
rs73075139	0.91[EUR][1000 genomes]
rs7515127	0.96[AFR][1000 genomes]
rs7519865	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7530862	0.91[ASW][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7531277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543376	0.92[JPT][hapmap]

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	nsv832514	chr1:211630247-211794963	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv1796467	chr1:211726975-211769893	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv1840920	chr1:211726975-211769893	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1836726	chr1:211736470-211752981	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv549125	chr1:211750362-211753094	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 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	chr1:211745800-211750800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:211747000-211750600	Weak transcription	Psoas Muscle	Psoas
3	chr1:211747200-211750800	Weak transcription	Spleen	Spleen
4	chr1:211747400-211750800	Weak transcription	Esophagus	oesophagus
5	chr1:211747600-211750600	Weak transcription	Right Ventricle	heart
6	chr1:211748000-211750400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:211748200-211750600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:211748400-211750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:211748600-211753200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:211748800-211750600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:211748800-211751000	Active TSS	Right Atrium	heart
12	chr1:211748800-211751400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:211749000-211750400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:211749000-211750400	Weak transcription	Thymus	Thymus
15	chr1:211749000-211750600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:211749000-211750600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:211749000-211750800	Active TSS	Fetal Intestine Small	intestine
18	chr1:211749000-211753400	Active TSS	Aorta	Aorta
19	chr1:211749000-211753400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:211749200-211750400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:211749200-211750800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:211749400-211750400	Active TSS	Fetal Brain Female	brain
23	chr1:211749400-211750600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:211749400-211750600	Active TSS	Brain Anterior Caudate	brain
25	chr1:211749400-211750600	Active TSS	Brain Hippocampus Middle	brain
26	chr1:211749400-211750600	Weak transcription	Placenta	Placenta
27	chr1:211749400-211750800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:211749400-211751400	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:211749400-211753200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:211749400-211753200	Active TSS	Fetal Stomach	stomach
31	chr1:211749400-211753200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:211749400-211753400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:211749600-211750400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:211749600-211750400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:211749600-211750400	Enhancers	Fetal Lung	lung
36	chr1:211749600-211750400	Weak transcription	Fetal Thymus	thymus
37	chr1:211749600-211750400	Weak transcription	Stomach Mucosa	stomach
38	chr1:211749600-211750600	Enhancers	Primary B cells from cord blood	blood
39	chr1:211749600-211750600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:211749600-211750600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:211749600-211750600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:211749600-211750600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:211749600-211750600	Flanking Active TSS	HUVEC	blood vessel
44	chr1:211749600-211750800	Weak transcription	Gastric	stomach
45	chr1:211749600-211750800	Weak transcription	Left Ventricle	heart
46	chr1:211749600-211750800	Weak transcription	Lung	lung
47	chr1:211749600-211750800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:211749600-211750800	Active TSS	HepG2	liver
49	chr1:211749600-211751000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:211749600-211753000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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