Variant report

Variant	rs1870098
Chromosome Location	chr10:28541396-28541397
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	chr10:28532869..28536330-chr10:28540569..28543040,3	MCF-7	breast:
2	chr10:28538163..28546243-chr10:28589319..28594336,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10508736	0.83[CEU][hapmap]
rs10763646	0.83[CEU][hapmap]
rs10763647	0.83[CEU][hapmap]
rs10763648	0.83[CEU][hapmap]
rs10763649	0.83[CEU][hapmap]
rs10763650	0.82[CEU][hapmap]
rs10763654	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10763655	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10763658	0.86[ASN][1000 genomes]
rs10826424	0.83[CEU][hapmap]
rs10826425	0.82[JPT][hapmap]
rs10826433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826435	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826436	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826449	0.86[CHB][hapmap]
rs11006917	0.83[CEU][hapmap]
rs11006946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006947	0.82[AFR][1000 genomes]
rs11006950	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs11006953	0.82[AFR][1000 genomes]
rs11006956	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006959	0.93[ASN][1000 genomes]
rs11006962	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11006965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006970	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1144513	0.81[ASN][1000 genomes]
rs1148175	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs12049636	0.83[CEU][hapmap]
rs1418757	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1418759	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs17758855	0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1870097	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937807	0.83[CEU][hapmap]
rs1937808	0.83[CEU][hapmap]
rs1937809	0.83[CEU][hapmap]
rs1953322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1953324	0.93[ASN][1000 genomes]
rs2085471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100615	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2100616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124955	0.82[CHB][hapmap]
rs2290701	0.88[ASN][1000 genomes]
rs2607540	0.86[CHB][hapmap]
rs2801833	0.83[CEU][hapmap]
rs2801835	0.83[CEU][hapmap]
rs2985535	0.83[CEU][hapmap]
rs2997210	0.83[CEU][hapmap]
rs3847388	0.86[CHB][hapmap]
rs61845911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6481515	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs7072480	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088465	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7096944	0.83[CEU][hapmap]
rs7893311	0.83[CEU][hapmap]
rs7905490	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs7913970	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs9919516	0.86[ASN][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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28519000-28552000	Weak transcription	Fetal Stomach	stomach
2	chr10:28521800-28544400	Weak transcription	Pancreas	Pancrea
3	chr10:28535800-28551600	Weak transcription	Fetal Intestine Small	intestine
4	chr10:28537400-28552600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:28537600-28543000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:28537600-28549400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr10:28537600-28552600	Weak transcription	Primary T cells from cord blood	blood
8	chr10:28537800-28541800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:28537800-28541800	Weak transcription	Esophagus	oesophagus
10	chr10:28537800-28542800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:28537800-28543000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:28537800-28543000	Weak transcription	Primary B cells from cord blood	blood
13	chr10:28537800-28543200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:28537800-28543600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:28537800-28550200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:28538000-28542200	Weak transcription	HMEC	breast
17	chr10:28538000-28542200	Weak transcription	NHEK	skin
18	chr10:28538000-28542400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:28538000-28543000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:28538000-28543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:28538000-28543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:28538800-28541400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:28538800-28544400	Weak transcription	Left Ventricle	heart
24	chr10:28539800-28543200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:28540000-28542400	Weak transcription	Hela-S3	cervix
26	chr10:28540000-28544200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr10:28540200-28543200	Weak transcription	HSMM	muscle
28	chr10:28540400-28543200	Weak transcription	Osteobl	bone
29	chr10:28540400-28544200	Enhancers	Rectal Smooth Muscle	rectum
30	chr10:28540600-28541600	Enhancers	Aorta	Aorta
31	chr10:28540600-28542000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:28540800-28541400	Weak transcription	HSMMtube	muscle
33	chr10:28540800-28541600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr10:28541000-28542000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr10:28541200-28542400	Enhancers	Fetal Heart	heart
36	chr10:28541200-28542400	Enhancers	Psoas Muscle	Psoas
37	chr10:28541200-28543400	Enhancers	Colon Smooth Muscle	Colon
38	chr10:28541200-28543800	Enhancers	Stomach Smooth Muscle	stomach

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