Variant report

Variant	rs12245003
Chromosome Location	chr10:112782529-112782530
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	chr10:112776495..112778257-chr10:112780884..112782883,2	K562	blood:
2	chr10:112677296..112679780-chr10:112780580..112783275,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHOC2-1	chr10:112778764-112782745	NONHSAT016379

Variant related genes	Relation type
ENSG00000108061	Chromatin interaction
ENSG00000214413	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11195357	0.88[JPT][hapmap];0.88[YRI][hapmap]
rs11195367	0.83[AFR][1000 genomes]
rs11195378	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11195384	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11195386	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11195389	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11195392	0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11195393	0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11195402	0.88[AFR][1000 genomes]
rs12244153	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12244273	0.85[AFR][1000 genomes]
rs12248431	0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12248632	0.83[ASN][1000 genomes]
rs12249521	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12249906	0.82[AFR][1000 genomes]
rs12253950	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12256152	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12258923	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs12264063	0.80[AFR][1000 genomes]
rs12266042	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12267661	0.82[ASN][1000 genomes]
rs12268160	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12268606	0.82[AFR][1000 genomes]
rs1327552	1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13306146	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1410052	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs17128099	1.00[YRI][hapmap]
rs17128102	0.88[YRI][hapmap]
rs17128270	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17128355	0.88[AFR][1000 genomes]
rs1800038	0.88[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3750621	0.89[AFR][1000 genomes]
rs3750622	0.89[AFR][1000 genomes]
rs4917593	0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4918610	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4918620	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918622	0.80[AFR][1000 genomes]
rs55879225	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56005122	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56302131	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56350255	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs59265487	0.80[AFR][1000 genomes]
rs72819772	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804245	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1051595	chr10:112730022-112789048	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:112707200-112784200	Weak transcription	Left Ventricle	heart
3	chr10:112723200-112783000	Weak transcription	Small Intestine	intestine
4	chr10:112732600-112789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:112732800-112782800	Weak transcription	Esophagus	oesophagus
6	chr10:112732800-112789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:112738000-112782800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:112738200-112784600	Weak transcription	Ovary	ovary
9	chr10:112740400-112791800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:112746000-112783400	Weak transcription	Colonic Mucosa	Colon
11	chr10:112746800-112782800	Weak transcription	Psoas Muscle	Psoas
12	chr10:112747600-112785200	Weak transcription	Fetal Brain Female	brain
13	chr10:112749200-112789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:112750400-112785000	Weak transcription	A549	lung
15	chr10:112753200-112782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:112753200-112784200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:112753400-112789600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:112754000-112784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:112754400-112782600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:112758200-112783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:112761600-112782800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr10:112761800-112784200	Weak transcription	Spleen	Spleen
23	chr10:112764400-112783000	Weak transcription	Brain Substantia Nigra	brain
24	chr10:112764800-112782600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:112765000-112782800	Weak transcription	Aorta	Aorta
26	chr10:112765000-112794200	Weak transcription	NH-A	brain
27	chr10:112765000-112794400	Weak transcription	NHLF	lung
28	chr10:112765200-112782600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr10:112765200-112794200	Weak transcription	NHEK	skin
30	chr10:112769800-112785600	Weak transcription	HUVEC	blood vessel
31	chr10:112770000-112782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:112770800-112798800	Weak transcription	HMEC	breast
33	chr10:112771600-112784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:112772200-112783000	Strong transcription	Primary B cells from cord blood	blood
35	chr10:112772800-112789200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr10:112773000-112784000	Weak transcription	Dnd41	blood
37	chr10:112773000-112793200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:112773000-112794000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:112776200-112783200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:112776800-112783200	Strong transcription	Adipose Nuclei	Adipose
41	chr10:112776800-112783400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:112777000-112783200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:112777200-112783800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr10:112777600-112783400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr10:112778000-112784400	Weak transcription	Placenta	Placenta
46	chr10:112778200-112783200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr10:112778400-112783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:112778400-112783600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:112778600-112782800	Weak transcription	Primary T cells from cord blood	blood
50	chr10:112778600-112789000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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