Variant report

Variant	rs7579181
Chromosome Location	chr2:10549357-10549358
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:41)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:41 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10544615..10547096-chr2:10548655..10551250,3	K562	blood:
2	chr2:10548741..10551044-chr2:10552688..10554394,2	K562	blood:
3	chr2:10261171..10265935-chr2:10544190..10551018,10	K562	blood:
4	chr2:10328150..10328991-chr2:10548904..10549863,5	MCF-7	breast:
5	chr2:10410359..10411311-chr2:10549026..10549739,3	MCF-7	breast:
6	chr2:10440924..10446095-chr2:10544022..10551736,19	MCF-7	breast:
7	chr2:10418216..10420909-chr2:10547555..10550904,3	K562	blood:
8	chr2:10472884..10475562-chr2:10547169..10549759,2	K562	blood:
9	chr2:10272011..10278010-chr2:10546327..10552012,10	K562	blood:
10	chr2:10445047..10447239-chr2:10547484..10549906,2	MCF-7	breast:
11	chr2:10416484..10418101-chr2:10547563..10549707,2	MCF-7	breast:
12	chr2:10266037..10268714-chr2:10547903..10550604,2	K562	blood:
13	chr2:10442822..10444429-chr2:10547773..10549369,2	K562	blood:
14	chr2:10480270..10481880-chr2:10548259..10550783,2	MCF-7	breast:
15	chr2:10461532..10462376-chr2:10549061..10549873,2	MCF-7	breast:
16	chr2:10423718..10426925-chr2:10546888..10550753,3	MCF-7	breast:
17	chr2:10265098..10266000-chr2:10549288..10549837,2	MCF-7	breast:
18	chr2:10548229..10551901-chr2:10552572..10557970,6	K562	blood:
19	chr2:10531886..10534694-chr2:10548127..10550273,2	K562	blood:
20	chr2:10544615..10546165-chr2:10548581..10550648,2	K562	blood:
21	chr2:10379794..10381312-chr2:10548728..10550420,2	K562	blood:
22	chr2:10328455..10329154-chr2:10549215..10549757,2	K562	blood:
23	chr2:10410367..10411323-chr2:10548606..10549914,5	K562	blood:
24	chr2:10537541..10541103-chr2:10547321..10550436,3	MCF-7	breast:
25	chr2:10436642..10438745-chr2:10547775..10550649,2	K562	blood:
26	chr2:10442266..10443520-chr2:10548955..10549705,3	MCF-7	breast:
27	chr2:10543950..10547023-chr2:10547884..10550475,4	MCF-7	breast:
28	chr2:10535204..10537517-chr2:10547562..10550495,2	MCF-7	breast:
29	chr2:10498534..10501300-chr2:10547746..10549393,2	K562	blood:
30	chr2:10547842..10550365-chr2:10556156..10557846,2	K562	blood:
31	chr2:10266037..10269086-chr2:10547903..10550826,4	K562	blood:
32	chr2:10460038..10463230-chr2:10546392..10550535,3	MCF-7	breast:
33	chr2:10270635..10275854-chr2:10544682..10552679,11	K562	blood:
34	chr2:10440762..10444214-chr2:10546694..10551810,5	K562	blood:
35	chr2:10212443..10213176-chr2:10548994..10549507,2	K562	blood:
36	chr2:10409982..10410924-chr2:10548925..10549650,2	MCF-7	breast:
37	chr15:93631076..93631748-chr2:10548940..10549868,2	MCF-7	breast:
38	chr2:10259324..10265273-chr2:10547206..10552383,9	K562	blood:
39	chr2:10548913..10551031-chr2:10587775..10589671,2	K562	blood:
40	chr2:10328070..10328961-chr2:10549008..10550652,5	MCF-7	breast:
41	chr2:10546710..10550413-chr2:10585616..10590159,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257135	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000264030	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11694643	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13383055	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs13383253	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs17434886	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270303	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3755261	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755262	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3771120	0.88[CHB][hapmap]
rs3771123	0.95[ASN][1000 genomes]
rs3771126	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771135	0.93[ASN][1000 genomes]
rs3771144	0.90[ASN][1000 genomes]
rs3771145	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3771146	0.88[ASN][1000 genomes]
rs3821197	0.88[CHB][hapmap]
rs3821199	0.83[CEU][hapmap]
rs3821200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55961729	0.91[ASN][1000 genomes]
rs56156675	0.91[ASN][1000 genomes]
rs56382508	0.91[ASN][1000 genomes]
rs62128251	0.90[ASN][1000 genomes]
rs62128252	0.90[ASN][1000 genomes]
rs62128254	0.90[ASN][1000 genomes]
rs62130179	0.90[ASN][1000 genomes]
rs62130183	0.90[ASN][1000 genomes]
rs62130187	0.98[ASN][1000 genomes]
rs62130191	0.91[ASN][1000 genomes]
rs7599203	0.90[ASN][1000 genomes]
rs7603265	1.00[ASN][1000 genomes]
rs7603352	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7608670	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9917369	0.88[CHB][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	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7579181	HPCAL1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10533000-10551800	Weak transcription	Ovary	ovary
2	chr2:10541200-10550800	Enhancers	Fetal Muscle Leg	muscle
3	chr2:10542000-10549400	Enhancers	HUVEC	blood vessel
4	chr2:10542400-10549400	Enhancers	NHDF-Ad	bronchial
5	chr2:10544200-10549600	Enhancers	Left Ventricle	heart
6	chr2:10544200-10549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:10544400-10549800	Enhancers	Right Ventricle	heart
8	chr2:10544600-10549400	Enhancers	Right Atrium	heart
9	chr2:10544800-10549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:10544800-10549600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:10544800-10549800	Enhancers	Lung	lung
12	chr2:10545200-10549800	Enhancers	Pancreas	Pancrea
13	chr2:10545400-10549600	Enhancers	Spleen	Spleen
14	chr2:10545400-10551800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:10545600-10549600	Enhancers	NH-A	brain
16	chr2:10545600-10549800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:10545800-10549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:10545800-10549800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:10545800-10550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:10546000-10549400	Enhancers	Osteobl	bone
21	chr2:10546200-10549800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:10546200-10550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:10546400-10551400	Enhancers	Fetal Thymus	thymus
24	chr2:10546600-10549800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr2:10546600-10550600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:10546800-10549400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:10546800-10549600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:10546800-10551400	Genic enhancers	Fetal Intestine Small	intestine
29	chr2:10547000-10549800	Enhancers	Adipose Nuclei	Adipose
30	chr2:10547000-10549800	Enhancers	Colon Smooth Muscle	Colon
31	chr2:10547000-10550200	Enhancers	Small Intestine	intestine
32	chr2:10547000-10551600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr2:10547200-10549600	Enhancers	Gastric	stomach
34	chr2:10547200-10551600	Enhancers	HSMM	muscle
35	chr2:10547400-10549400	Flanking Active TSS	Hela-S3	cervix
36	chr2:10547400-10549600	Weak transcription	Fetal Brain Female	brain
37	chr2:10547400-10551200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:10547400-10551400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:10547600-10549400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr2:10547600-10549400	Flanking Active TSS	A549	lung
41	chr2:10547600-10550800	Enhancers	Fetal Intestine Large	intestine
42	chr2:10547600-10551000	Enhancers	Primary B cells from peripheral blood	blood
43	chr2:10547600-10551600	Enhancers	Fetal Lung	lung
44	chr2:10547800-10549400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:10547800-10549800	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr2:10547800-10551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:10548000-10549400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr2:10548000-10549400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:10548000-10549400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:10548000-10549600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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