Variant report

Variant	rs60389428
Chromosome Location	chr1:9912509-9912510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9910251..9913174-chr1:9920173..9922421,2	K562	blood:
2	chr1:9884056..9886258-chr1:9911889..9914229,2	MCF-7	breast:
3	chr1:9910788..9913768-chr6:58778329..58780695,2	MCF-7	breast:
4	chr1:9907709..9909733-chr1:9912476..9914067,2	K562	blood:

Variant related genes	Relation type
ENSG00000223989	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11121499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11809921	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1220408	0.84[ASN][1000 genomes]
rs15177	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17034420	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033960	0.86[EUR][1000 genomes]
rs2278611	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3860318	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888014	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56315207	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57979292	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58281392	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59341676	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59530761	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59533551	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60547803	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60624175	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61785229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61785586	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61785590	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6658583	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695334	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858068	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74054138	0.85[AMR][1000 genomes]
rs7529783	0.85[AMR][1000 genomes]
rs7533225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9896000-9919200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:9896600-9913400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:9902800-9913600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:9904000-9913000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
6	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
7	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:9904400-9913400	Weak transcription	Fetal Lung	lung
9	chr1:9904400-9922600	Weak transcription	Pancreas	Pancrea
10	chr1:9904400-9923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
12	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:9904600-9922600	Weak transcription	Ovary	ovary
14	chr1:9904600-9935000	Weak transcription	Osteobl	bone
15	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
16	chr1:9905200-9915400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:9906600-9927400	Weak transcription	Liver	Liver
18	chr1:9907000-9913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:9907000-9913400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:9907000-9919200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:9907400-9913600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:9907400-9914200	Strong transcription	Adipose Nuclei	Adipose
24	chr1:9907400-9929800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:9908200-9913400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:9908200-9915000	Strong transcription	Fetal Stomach	stomach
27	chr1:9908400-9912800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:9908400-9913800	Strong transcription	Esophagus	oesophagus
29	chr1:9908800-9913600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:9909400-9912600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:9909600-9912800	Strong transcription	Gastric	stomach
32	chr1:9909600-9913400	Enhancers	Fetal Brain Male	brain
33	chr1:9909800-9915000	Strong transcription	HepG2	liver
34	chr1:9910000-9912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:9910000-9913200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:9910000-9935000	Weak transcription	NHLF	lung
37	chr1:9910200-9912800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:9910200-9912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:9910200-9918400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:9910600-9913200	Enhancers	Brain Cingulate Gyrus	brain
41	chr1:9910800-9913000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:9910800-9913200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:9910800-9913200	Enhancers	Brain Anterior Caudate	brain
44	chr1:9910800-9913600	Enhancers	Fetal Brain Female	brain
45	chr1:9910800-9913800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:9911000-9918400	Weak transcription	Left Ventricle	heart
47	chr1:9911000-9919600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:9911000-9927400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:9911000-9930400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:9911200-9912800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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