Variant report

Variant	rs185669
Chromosome Location	chr10:25238456-25238457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:25235302..25239090-chr10:25240000..25243649,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099256	Chromatin interaction
ENSG00000273107	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10741071	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs10741072	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.89[ASN][1000 genomes]
rs10764513	0.81[ASN][1000 genomes]
rs10764515	0.80[CEU][hapmap]
rs10828728	1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs10828730	0.81[ASN][1000 genomes]
rs10828731	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs10828751	0.80[CEU][hapmap]
rs11014314	0.84[ASN][1000 genomes]
rs11014318	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11014320	0.93[ASN][1000 genomes]
rs200730	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2035888	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2279547	0.80[CEU][hapmap]
rs2478091	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274295	0.84[ASN][1000 genomes]
rs274296	0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs274297	0.85[ASN][1000 genomes]
rs274299	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274300	0.85[ASN][1000 genomes]
rs274301	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs274302	0.82[JPT][hapmap]
rs274303	0.81[EUR][1000 genomes]
rs274304	0.88[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs274305	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs274306	0.81[EUR][1000 genomes]
rs274307	0.81[ASN][1000 genomes]
rs274308	0.81[EUR][1000 genomes]
rs274309	0.81[EUR][1000 genomes]
rs274310	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs274311	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap]
rs274312	0.81[EUR][1000 genomes]
rs274313	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs274316	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3000491	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748223	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.89[ASN][1000 genomes]
rs6482468	0.84[CEU][hapmap]

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	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs185669	OTUD1	cis	parietal	SCAN
rs185669	THNSL1	cis	parietal	SCAN
rs185669	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25191600-25240600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:25211400-25239800	Weak transcription	Fetal Kidney	kidney
3	chr10:25215800-25240000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr10:25219200-25240000	Weak transcription	Dnd41	blood
5	chr10:25225400-25240000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:25225400-25240000	Weak transcription	Fetal Brain Female	brain
7	chr10:25226200-25239800	Weak transcription	Fetal Lung	lung
8	chr10:25226400-25239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:25228200-25239800	Weak transcription	Fetal Stomach	stomach
10	chr10:25232600-25239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:25232800-25240000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:25234200-25240400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:25234200-25240400	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:25234200-25240600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr10:25234200-25240600	Weak transcription	Right Atrium	heart
16	chr10:25234400-25239800	Weak transcription	A549	lung
17	chr10:25234400-25239800	Weak transcription	HepG2	liver
18	chr10:25234400-25239800	Weak transcription	K562	blood
19	chr10:25234400-25240600	Weak transcription	Adipose Nuclei	Adipose
20	chr10:25234600-25239800	Weak transcription	Fetal Intestine Small	intestine
21	chr10:25235400-25240400	Enhancers	Brain Substantia Nigra	brain
22	chr10:25236200-25241000	Weak transcription	Thymus	Thymus
23	chr10:25236600-25240200	Weak transcription	NHLF	lung
24	chr10:25236800-25239400	Enhancers	Brain Hippocampus Middle	brain
25	chr10:25236800-25239800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:25236800-25240000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:25236800-25240600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr10:25236800-25240600	Weak transcription	Left Ventricle	heart
29	chr10:25237000-25238800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:25237000-25239800	Weak transcription	Fetal Muscle Leg	muscle
31	chr10:25237000-25240000	Weak transcription	Small Intestine	intestine
32	chr10:25237000-25240200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:25237000-25240400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:25237000-25240400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:25237000-25240400	Weak transcription	Pancreas	Pancrea
36	chr10:25237000-25240400	Weak transcription	Osteobl	bone
37	chr10:25237000-25240600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:25237000-25240600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:25237000-25240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:25237000-25240600	Weak transcription	NH-A	brain
41	chr10:25237000-25240800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:25237000-25241000	Weak transcription	Ovary	ovary
43	chr10:25237200-25240000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:25237200-25240000	Weak transcription	NHDF-Ad	bronchial
45	chr10:25237200-25240400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:25237200-25240400	Weak transcription	GM12878-XiMat	blood
47	chr10:25237200-25240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:25237200-25240600	Weak transcription	HUVEC	blood vessel
49	chr10:25237200-25240800	Weak transcription	HMEC	breast
50	chr10:25237400-25239000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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