Variant report

Variant	rs41307498
Chromosome Location	chr10:25402202-25402203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:25402201..25402709-chr10:25515764..25516442,2	K562	blood:
2	chr10:25402163..25402736-chr10:25722736..25723649,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR158-1	chr10:25401987-25402615	XLOC_008414
2	lnc-GPR158-1	chr10:25401987-25402615	ENSG00000231422.2
3	lnc-GPR158-1	chr10:25401987-25402615	NONHSAT011799

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1124490	0.93[EUR][1000 genomes]
rs12241288	0.93[EUR][1000 genomes]
rs12248877	0.93[EUR][1000 genomes]
rs12261100	0.86[EUR][1000 genomes]
rs1388926	0.86[EUR][1000 genomes]
rs1409305	0.93[EUR][1000 genomes]
rs1552772	0.93[EUR][1000 genomes]
rs16925193	0.93[EUR][1000 genomes]
rs16925198	0.93[EUR][1000 genomes]
rs3808907	0.81[EUR][1000 genomes]
rs41279882	0.93[EUR][1000 genomes]
rs41279886	0.93[EUR][1000 genomes]
rs41279890	0.93[EUR][1000 genomes]
rs41279894	0.93[EUR][1000 genomes]
rs41304607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55788231	1.00[EUR][1000 genomes]
rs57639701	0.93[EUR][1000 genomes]
rs57642444	0.93[EUR][1000 genomes]
rs57695610	0.93[EUR][1000 genomes]
rs58164169	0.81[EUR][1000 genomes]
rs58320082	0.93[EUR][1000 genomes]
rs59189661	0.93[EUR][1000 genomes]
rs59876862	0.86[EUR][1000 genomes]
rs60880723	0.93[EUR][1000 genomes]
rs61278248	0.93[EUR][1000 genomes]
rs61585865	0.93[EUR][1000 genomes]
rs6482464	0.93[EUR][1000 genomes]
rs7072278	0.86[EUR][1000 genomes]
rs7073171	0.86[EUR][1000 genomes]
rs7075327	0.93[EUR][1000 genomes]
rs7080371	0.86[EUR][1000 genomes]
rs7083691	0.86[EUR][1000 genomes]
rs7099168	0.93[EUR][1000 genomes]
rs73606594	0.85[EUR][1000 genomes]
rs73606599	0.93[EUR][1000 genomes]
rs73606600	0.93[EUR][1000 genomes]
rs73608203	0.93[EUR][1000 genomes]
rs73608204	0.93[EUR][1000 genomes]
rs73608206	0.93[EUR][1000 genomes]
rs73608208	0.93[EUR][1000 genomes]
rs73608210	0.86[EUR][1000 genomes]
rs73608211	0.93[EUR][1000 genomes]
rs73608212	0.93[EUR][1000 genomes]
rs73608213	0.93[EUR][1000 genomes]
rs73608214	0.86[EUR][1000 genomes]
rs73608216	0.86[EUR][1000 genomes]
rs73608217	0.86[EUR][1000 genomes]
rs73608218	0.86[EUR][1000 genomes]
rs73608219	0.86[EUR][1000 genomes]
rs73608223	0.93[EUR][1000 genomes]
rs73608224	0.93[EUR][1000 genomes]
rs73608225	0.93[EUR][1000 genomes]
rs73608226	0.81[EUR][1000 genomes]
rs73608229	0.93[EUR][1000 genomes]
rs73608233	0.93[EUR][1000 genomes]
rs73608234	0.93[EUR][1000 genomes]
rs73608235	0.93[EUR][1000 genomes]
rs73608236	0.93[EUR][1000 genomes]
rs73608237	0.93[EUR][1000 genomes]
rs73608238	0.93[EUR][1000 genomes]
rs73608239	0.93[EUR][1000 genomes]
rs73608240	0.93[EUR][1000 genomes]
rs73608241	0.93[EUR][1000 genomes]
rs7905478	0.93[EUR][1000 genomes]
rs7920527	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9663998	0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894970	chr10:25385858-25522280	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25392400-25414200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:25395000-25402400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:25395000-25405000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:25397400-25404800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr10:25398000-25402400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:25398200-25404600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr10:25398400-25402400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:25398400-25402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:25400400-25403400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:25401600-25402600	Enhancers	Fetal Brain Female	brain
11	chr10:25401600-25402800	Enhancers	Brain Angular Gyrus	brain
12	chr10:25401800-25402600	Enhancers	Fetal Brain Male	brain
13	chr10:25401800-25403200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:25401800-25403400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:25401800-25403400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr10:25402000-25402600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr10:25402000-25402600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr10:25402000-25402600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:25402000-25402600	Active TSS	Brain Cingulate Gyrus	brain
20	chr10:25402000-25402600	Enhancers	Duodenum Mucosa	Duodenum
21	chr10:25402000-25402600	Enhancers	Pancreas	Pancrea
22	chr10:25402000-25402600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr10:25402000-25402800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:25402000-25403200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:25402000-25403200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:25402000-25403200	Enhancers	Adipose Nuclei	Adipose
27	chr10:25402000-25403200	Enhancers	A549	lung
28	chr10:25402000-25403400	Enhancers	Stomach Mucosa	stomach
29	chr10:25402000-25403400	Enhancers	HMEC	breast
30	chr10:25402200-25402400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr10:25402200-25402400	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr10:25402200-25402400	Active TSS	Brain Anterior Caudate	brain
33	chr10:25402200-25402400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr10:25402200-25402600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:25402200-25402600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr10:25402200-25402600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:25402200-25402600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:25402200-25402600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr10:25402200-25402600	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr10:25402200-25402600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr10:25402200-25402600	Active TSS	Brain Substantia Nigra	brain
42	chr10:25402200-25402600	Enhancers	Esophagus	oesophagus
43	chr10:25402200-25402600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr10:25402200-25402600	Active TSS	Rectal Smooth Muscle	rectum
45	chr10:25402200-25402600	Enhancers	Osteobl	bone
46	chr10:25402200-25403200	Enhancers	HepG2	liver
47	chr10:25402200-25403600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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