Variant report

Variant	rs13383055
Chromosome Location	chr2:10556956-10556957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:10556936-10557109	A549	lung:	n/a	n/a
2	POLR2A	chr2:10554692-10557277	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10555615..10558543-chr2:10573607..10576166,2	K562	blood:
2	chr2:10547842..10550365-chr2:10556156..10557846,2	K562	blood:
3	chr2:10553085..10555070-chr2:10555415..10558932,3	MCF-7	breast:
4	chr2:10548229..10551901-chr2:10552572..10557970,6	K562	blood:
5	chr2:10265350..10268132-chr2:10555192..10558386,3	K562	blood:
6	chr2:10552751..10557401-chr2:10586002..10589007,6	K562	blood:

No data

Variant related genes	Relation type
HPCAL1	TF binding region
ENSG00000115758	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000257135	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11692055	0.80[ASN][1000 genomes]
rs11694643	0.95[ASN][1000 genomes]
rs13383253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428169	0.80[ASN][1000 genomes]
rs13430847	0.80[ASN][1000 genomes]
rs17434886	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs2270303	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs2270304	0.80[ASN][1000 genomes]
rs2270305	0.80[ASN][1000 genomes]
rs3732119	0.80[ASN][1000 genomes]
rs3755261	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs3755262	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs3771120	0.88[CHB][hapmap]
rs3771123	0.95[ASN][1000 genomes]
rs3771126	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs3771135	0.84[ASN][1000 genomes]
rs3771144	0.86[ASN][1000 genomes]
rs3771145	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs3771146	0.84[ASN][1000 genomes]
rs3821197	0.88[CHB][hapmap]
rs3821200	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs55961729	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156675	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382508	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62128251	0.86[ASN][1000 genomes]
rs62128252	0.86[ASN][1000 genomes]
rs62128254	0.86[ASN][1000 genomes]
rs62130179	0.86[ASN][1000 genomes]
rs62130183	0.86[ASN][1000 genomes]
rs62130187	0.88[ASN][1000 genomes]
rs62130191	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579181	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7599203	0.86[ASN][1000 genomes]
rs7603265	0.91[ASN][1000 genomes]
rs7603352	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7608670	0.86[CHB][hapmap]
rs9917369	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10549000-10570400	Weak transcription	Psoas Muscle	Psoas
2	chr2:10549400-10562200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:10549400-10563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:10549600-10562200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:10549600-10572400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:10549800-10561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:10549800-10562200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:10549800-10562600	Weak transcription	Esophagus	oesophagus
9	chr2:10549800-10563400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:10550200-10571800	Weak transcription	Small Intestine	intestine
11	chr2:10551200-10574800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:10551400-10564400	Weak transcription	Fetal Kidney	kidney
13	chr2:10551600-10557800	Enhancers	Pancreas	Pancrea
14	chr2:10552000-10559600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:10552200-10559600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:10552200-10559800	Weak transcription	Ovary	ovary
17	chr2:10552400-10558800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:10552800-10561400	Weak transcription	Primary B cells from cord blood	blood
19	chr2:10553000-10559400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:10553000-10559600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:10553000-10559600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:10553000-10559800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:10553000-10559800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:10553000-10559800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:10553000-10560200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:10553000-10573200	Weak transcription	K562	blood
27	chr2:10553400-10558200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:10553400-10559600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:10553600-10559800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:10553600-10561800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:10554000-10560000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:10554200-10557600	Weak transcription	A549	lung
33	chr2:10554400-10559800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:10554400-10562000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:10554400-10563000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:10554400-10566800	Weak transcription	NHLF	lung
37	chr2:10554400-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:10554600-10557600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:10554600-10565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:10554600-10579200	Weak transcription	NHDF-Ad	bronchial
41	chr2:10554800-10559400	Weak transcription	Liver	Liver
42	chr2:10554800-10560400	Weak transcription	Osteobl	bone
43	chr2:10554800-10561200	Weak transcription	Fetal Lung	lung
44	chr2:10554800-10565800	Weak transcription	Aorta	Aorta
45	chr2:10554800-10572600	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:10555000-10560000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:10555000-10560000	Weak transcription	Adipose Nuclei	Adipose
48	chr2:10555000-10560600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:10555000-10564400	Weak transcription	Hela-S3	cervix
50	chr2:10555200-10559600	Weak transcription	Primary T cells from cord blood	blood

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