Variant report

Variant	rs1028534
Chromosome Location	chr10:52228621-52228622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52227475..52229594-chr10:52231830..52233869,2	K562	blood:
2	chr10:52174561..52178391-chr10:52227208..52231708,4	MCF-7	breast:
3	chr10:52179209..52181843-chr10:52226952..52229570,2	MCF-7	breast:
4	chr10:52226760..52229659-chr10:52383902..52385556,2	K562	blood:
5	chr10:52227177..52229638-chr10:52267267..52268794,2	K562	blood:
6	chr10:52227035..52229845-chr10:52267079..52268728,2	MCF-7	breast:
7	chr10:52227444..52229529-chr10:52230846..52232373,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225303	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082515	0.91[JPT][hapmap]
rs10218880	1.00[CEU][hapmap]
rs10218927	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10826014	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs11005720	0.90[JPT][hapmap]
rs11005782	0.87[AMR][1000 genomes]
rs11006224	1.00[CEU][hapmap]
rs1203380	0.91[JPT][hapmap]
rs1212555	0.91[JPT][hapmap]
rs12243444	1.00[CEU][hapmap]
rs12261465	1.00[CEU][hapmap]
rs12262564	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12569801	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569909	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12573520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16937491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16937722	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16937771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937874	1.00[CEU][hapmap]
rs17179881	0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1880071	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064760	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2983346	0.92[ASN][1000 genomes]
rs2983349	0.93[ASN][1000 genomes]
rs3739990	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41427847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57015168	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57748270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57999700	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58383805	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58642196	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59510112	0.88[ASN][1000 genomes]
rs59512026	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66546375	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67761241	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
2	chr10:52192400-52230400	Weak transcription	HSMM	muscle
3	chr10:52197800-52229800	Weak transcription	Gastric	stomach
4	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
5	chr10:52208200-52229600	Weak transcription	Right Ventricle	heart
6	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:52209600-52229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:52211800-52229400	Weak transcription	NHEK	skin
9	chr10:52212800-52229400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:52212800-52229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:52215200-52228800	Weak transcription	HepG2	liver
13	chr10:52215200-52229000	Weak transcription	Brain Angular Gyrus	brain
14	chr10:52217200-52229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:52218200-52228800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr10:52218200-52230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:52218400-52229400	Weak transcription	A549	lung
19	chr10:52219800-52229000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr10:52220200-52230400	Weak transcription	Hela-S3	cervix
22	chr10:52220400-52228800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:52220400-52228800	Weak transcription	Primary B cells from cord blood	blood
24	chr10:52220400-52229000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr10:52220400-52229000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:52220400-52229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:52220400-52229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:52220400-52229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:52220400-52229000	Weak transcription	Placenta	Placenta
30	chr10:52220400-52229200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr10:52220400-52229200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:52220400-52229200	Weak transcription	Fetal Lung	lung
33	chr10:52220400-52229600	Weak transcription	Fetal Thymus	thymus
34	chr10:52220400-52229800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:52220400-52229800	Weak transcription	Lung	lung
36	chr10:52220400-52230200	Weak transcription	NHLF	lung
37	chr10:52220400-52237800	Weak transcription	Ovary	ovary
38	chr10:52220600-52229000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:52220600-52229000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:52220600-52229000	Weak transcription	Spleen	Spleen
41	chr10:52220600-52229200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr10:52220600-52229200	Weak transcription	Liver	Liver
43	chr10:52220600-52229400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:52220600-52229400	Weak transcription	Thymus	Thymus
45	chr10:52220600-52229600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:52220600-52229600	Weak transcription	Left Ventricle	heart
47	chr10:52220600-52229800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr10:52220600-52230400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr10:52220800-52229400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:52220800-52230000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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