Variant report

Variant	rs2480696
Chromosome Location	chr1:153506765-153506766
allele	A/G
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:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153506466..153507372-chr15:22833387..22834013,2	Hela-S3	cervix:
2	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
3	chr1:153505806..153506777-chr19:49468486..49469085,2	Hela-S3	cervix:
4	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
5	chr1:153506426..153507317-chr11:64863456..64864140,2	Hela-S3	cervix:
6	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
7	chr1:153506311..153507076-chr11:66845468..66846068,2	Hela-S3	cervix:
8	chr1:153506255..153507024-chr19:14628743..14629408,2	Hela-S3	cervix:
9	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
10	chr1:153506112..153506833-chr11:65430861..65431455,2	Hela-S3	cervix:
11	chr1:40626432..40627384-chr1:153506329..153507084,2	Hela-S3	cervix:
12	chr1:153505924..153506825-chr15:65596692..65597194,2	Hela-S3	cervix:
13	chr1:153506112..153507037-chr3:15643228..15643930,3	Hela-S3	cervix:
14	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
15	chr1:153506146..153507102-chr4:83822420..83823343,2	Hela-S3	cervix:
16	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
17	chr1:153506244..153507175-chr19:55895900..55896430,2	Hela-S3	cervix:
18	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
19	chr1:153505866..153506777-chr14:75745220..75746209,2	Hela-S3	cervix:
20	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
21	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
22	chr1:153505831..153506827-chr15:59041415..59041985,2	Hela-S3	cervix:
23	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
24	chr1:153506299..153508188-chr1:153578857..153582741,3	K562	blood:
25	chr1:153506556..153507277-chr12:113659217..113659722,2	HCT-116	colon:
26	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
27	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
28	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:
29	chr1:153506069..153506861-chr9:140135286..140136179,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000233493	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000153575	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000131373	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000186815	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000087086	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000169814	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000117000	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000137845	Chromatin interaction

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

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

rs_ID	r²[population]
rs16835393	0.83[AMR][1000 genomes]
rs2094217	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2480695	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28483109	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762262	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477339	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4845352	0.82[EUR][1000 genomes]
rs4845554	0.83[AMR][1000 genomes]
rs532652	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587745	0.83[AMR][1000 genomes]
rs6587746	0.83[AMR][1000 genomes]
rs659403	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684970	0.81[EUR][1000 genomes]
rs7518306	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9426945	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.89[AMR][1000 genomes];0.85[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
3	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
4	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:153504400-153506800	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:153504400-153507000	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:153504800-153507200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:153504800-153507200	Enhancers	Spleen	Spleen
9	chr1:153504800-153507800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:153504800-153507800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:153505000-153506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:153505000-153507000	Flanking Active TSS	Hela-S3	cervix
14	chr1:153505000-153507400	Enhancers	Liver	Liver
15	chr1:153505400-153506800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:153505400-153506800	Flanking Active TSS	Stomach Mucosa	stomach
17	chr1:153505400-153507400	Enhancers	Pancreas	Pancrea
18	chr1:153505400-153507600	Enhancers	Fetal Lung	lung
19	chr1:153505400-153507600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:153505400-153507800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:153505400-153507800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:153505400-153507800	Flanking Active TSS	HUVEC	blood vessel
23	chr1:153505400-153508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr1:153505400-153508000	Enhancers	Fetal Heart	heart
25	chr1:153505400-153508200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:153505400-153508200	Flanking Active TSS	Colonic Mucosa	Colon
27	chr1:153505400-153508400	Flanking Active TSS	NH-A	brain
28	chr1:153505600-153506800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr1:153505600-153506800	Flanking Active TSS	NHEK	skin
30	chr1:153505600-153507000	Flanking Active TSS	HSMMtube	muscle
31	chr1:153505600-153508000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:153505600-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:153505800-153506800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:153505800-153506800	Flanking Active TSS	Right Atrium	heart
35	chr1:153505800-153507000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:153505800-153507000	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr1:153505800-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:153505800-153508400	Flanking Active TSS	Osteobl	bone
39	chr1:153505800-153509200	Active TSS	Aorta	Aorta
40	chr1:153505800-153509400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr1:153506000-153506800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:153506000-153506800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:153506000-153507000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:153506000-153507000	Flanking Active TSS	Left Ventricle	heart
45	chr1:153506000-153507200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
46	chr1:153506000-153507400	Enhancers	Gastric	stomach
47	chr1:153506000-153507800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:153506000-153507800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr1:153506000-153508000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr1:153506000-153508000	Transcr. at gene 5' and 3'	NHLF	lung

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