Variant report

Variant	rs10178025
Chromosome Location	chr2:58296326-58296327
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58288525..58290696-chr2:58296073..58298734,2	K562	blood:
2	chr2:58295348..58297544-chr2:58301937..58304315,2	MCF-7	breast:
3	chr2:58293383..58297063-chr2:58301536..58303985,3	K562	blood:
4	chr2:58292161..58293709-chr2:58295518..58297243,2	MCF-7	breast:
5	chr2:58272740..58275363-chr2:58295743..58298004,2	MCF-7	breast:
6	chr2:58286306..58289261-chr2:58295649..58298415,2	K562	blood:

Variant related genes	Relation type
ENSG00000251738	Chromatin interaction
ENSG00000028116	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10165760	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10174202	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176681	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176942	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10182762	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10187411	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10203014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025755	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11883874	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11891477	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11892302	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12104650	0.80[AFR][1000 genomes]
rs13382369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394820	0.99[AFR][1000 genomes]
rs13405281	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13410500	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13419989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13431271	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1371213	0.89[AMR][1000 genomes]
rs17049333	1.00[ASN][1000 genomes]
rs17049337	1.00[ASN][1000 genomes]
rs17049338	1.00[ASN][1000 genomes]
rs17049414	1.00[ASN][1000 genomes]
rs2165100	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2165103	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2312486	0.89[AMR][1000 genomes]
rs28521626	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4459722	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57112138	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57597086	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58470176	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60364084	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6718190	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716758	0.89[AMR][1000 genomes]
rs72949131	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949137	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949158	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72951042	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951048	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951056	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73944804	0.93[AFR][1000 genomes]
rs7563312	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7569731	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7574578	1.00[AMR][1000 genomes]
rs7574694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7577402	1.00[ASN][1000 genomes]
rs7600213	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9973345	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9973928	0.94[AFR][1000 genomes];0.89[AMR][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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58274600-58298600	Weak transcription	Spleen	Spleen
2	chr2:58274600-58302400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:58274800-58296400	Weak transcription	Ovary	ovary
4	chr2:58274800-58296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:58274800-58302200	Weak transcription	Aorta	Aorta
6	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:58275000-58297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:58275000-58302600	Weak transcription	Esophagus	oesophagus
9	chr2:58275000-58302800	Weak transcription	Fetal Stomach	stomach
10	chr2:58275000-58305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
14	chr2:58275800-58316800	Weak transcription	HMEC	breast
15	chr2:58279000-58319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:58279400-58315600	Weak transcription	Dnd41	blood
17	chr2:58281000-58297800	Weak transcription	Fetal Lung	lung
18	chr2:58282400-58300400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:58282400-58301400	Weak transcription	Lung	lung
20	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:58283400-58296600	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:58283600-58298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:58284200-58296400	Weak transcription	Left Ventricle	heart
24	chr2:58284200-58303800	Weak transcription	Gastric	stomach
25	chr2:58284200-58317600	Weak transcription	HepG2	liver
26	chr2:58284400-58325000	Weak transcription	NHEK	skin
27	chr2:58285200-58317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:58286000-58296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:58286200-58297400	Weak transcription	Adipose Nuclei	Adipose
30	chr2:58286200-58297400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:58286200-58302200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:58286200-58317600	Weak transcription	K562	blood
33	chr2:58286400-58302000	Weak transcription	Hela-S3	cervix
34	chr2:58286400-58317600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:58287200-58298400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:58287200-58315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:58288200-58311000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:58289400-58300000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:58289400-58300200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:58290000-58301000	Weak transcription	Placenta	Placenta
41	chr2:58290400-58315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:58290800-58296400	Weak transcription	Liver	Liver
43	chr2:58291200-58296400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:58291200-58297400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:58291200-58299600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:58291200-58301800	Weak transcription	Thymus	Thymus
47	chr2:58291200-58316400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:58291400-58302200	Weak transcription	Brain Substantia Nigra	brain
49	chr2:58291400-58302200	Weak transcription	Fetal Heart	heart
50	chr2:58291600-58296400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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