Variant report

Variant	rs2480785
Chromosome Location	chr1:10569258-10569259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10566900..10569422-chr1:10571271..10572995,2	K562	blood:
2	chr1:10568543..10570422-chr1:10582522..10585336,2	K562	blood:
3	chr1:10567638..10569716-chr1:10700234..10702656,2	K562	blood:
4	chr1:10568015..10570793-chr1:10754272..10755934,2	MCF-7	breast:
5	chr1:10534928..10537211-chr1:10567744..10569324,3	K562	blood:
6	chr1:10568670..10571119-chr1:10926842..10928478,2	K562	blood:
7	chr1:10566008..10570273-chr1:10573569..10578315,6	K562	blood:
8	chr1:10567723..10570074-chr1:10684964..10687923,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000130940	Chromatin interaction
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11121587	0.88[EUR][1000 genomes]
rs1152739	0.85[EUR][1000 genomes]
rs1188525	0.87[EUR][1000 genomes]
rs1188526	0.87[EUR][1000 genomes]
rs12028449	0.88[EUR][1000 genomes]
rs12375	0.90[EUR][1000 genomes]
rs1411402	0.98[EUR][1000 genomes]
rs1632108	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17035305	0.88[EUR][1000 genomes]
rs2026792	0.90[EUR][1000 genomes]
rs2056417	0.98[EUR][1000 genomes]
rs2150038	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2480777	0.90[EUR][1000 genomes]
rs2483677	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2506880	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2506889	0.90[EUR][1000 genomes]
rs2506892	0.90[EUR][1000 genomes]
rs2506896	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2506901	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2781232	0.87[EUR][1000 genomes]
rs2847344	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34575776	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4846235	0.88[EUR][1000 genomes]
rs585870	0.87[EUR][1000 genomes]
rs587916	0.87[EUR][1000 genomes]
rs589400	0.88[EUR][1000 genomes]
rs596537	0.88[EUR][1000 genomes]
rs597438	0.88[EUR][1000 genomes]
rs607941	0.87[EUR][1000 genomes]
rs616402	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616488	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs617728	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620405	0.88[EUR][1000 genomes]
rs622623	0.88[EUR][1000 genomes]
rs648324	0.88[EUR][1000 genomes]
rs648399	0.88[EUR][1000 genomes]
rs652771	0.87[EUR][1000 genomes]
rs6540933	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs660725	0.87[EUR][1000 genomes]
rs662064	0.86[EUR][1000 genomes]
rs668805	0.87[EUR][1000 genomes]
rs669701	0.87[EUR][1000 genomes]
rs67488812	0.88[EUR][1000 genomes]
rs683864	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9430149	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv8435	chr1:10568184-10572374	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10555200-10570000	Weak transcription	Aorta	Aorta
2	chr1:10555600-10570400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:10555600-10570400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:10555600-10570600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:10555800-10569600	Weak transcription	Colonic Mucosa	Colon
6	chr1:10555800-10570400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:10556000-10569400	Weak transcription	Fetal Brain Female	brain
8	chr1:10556000-10570200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:10556400-10570200	Weak transcription	Fetal Kidney	kidney
10	chr1:10556600-10570000	Weak transcription	Right Ventricle	heart
11	chr1:10556600-10570400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:10556600-10570400	Weak transcription	Stomach Mucosa	stomach
13	chr1:10557000-10569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:10557600-10569600	Weak transcription	HMEC	breast
15	chr1:10557600-10569600	Weak transcription	NHEK	skin
16	chr1:10557800-10569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:10557800-10569600	Weak transcription	NHLF	lung
18	chr1:10559000-10570600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:10559200-10570200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:10562600-10570000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:10562600-10570200	Weak transcription	Small Intestine	intestine
22	chr1:10562600-10570600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:10562800-10570000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:10564800-10570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:10564800-10570400	Weak transcription	Right Atrium	heart
26	chr1:10564800-10570600	Weak transcription	Lung	lung
27	chr1:10566400-10577800	Enhancers	Fetal Thymus	thymus
28	chr1:10566800-10579800	Enhancers	Liver	Liver
29	chr1:10567000-10570000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:10567000-10570600	Enhancers	GM12878-XiMat	blood
31	chr1:10567200-10569800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:10567200-10570400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:10567200-10570600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:10567200-10570600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:10567400-10570000	Enhancers	Dnd41	blood
36	chr1:10567400-10570200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:10567400-10570200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:10567400-10570400	Enhancers	A549	lung
39	chr1:10567400-10570400	Enhancers	Osteobl	bone
40	chr1:10567400-10570600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:10567400-10571200	Enhancers	Fetal Muscle Leg	muscle
42	chr1:10567400-10572600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:10567600-10569800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:10567600-10570000	Weak transcription	Fetal Brain Male	brain
45	chr1:10567600-10570000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:10567600-10570000	Weak transcription	Spleen	Spleen
47	chr1:10567600-10570200	Weak transcription	Thymus	Thymus
48	chr1:10567600-10570400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:10567600-10570600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:10567600-10570600	Enhancers	Primary hematopoietic stem cells	blood

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