Variant report

Variant	rs3739990
Chromosome Location	chr10:52193333-52193334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52184358..52187257-chr10:52191960..52194304,3	K562	blood:
2	chr10:52189329..52191710-chr10:52192789..52194916,2	K562	blood:
3	chr10:52191418..52195182-chr10:52381701..52384353,3	MCF-7	breast:
4	chr10:52187426..52191274-chr10:52192997..52195335,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10082515	0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs10218880	1.00[CEU][hapmap]
rs10218927	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1028534	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]
rs10826014	0.91[JPT][hapmap]
rs11005720	0.90[JPT][hapmap]
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];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573520	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16937491	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16937722	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16937771	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16937775	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16937786	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16937874	1.00[CEU][hapmap]
rs17179881	0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1880071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064760	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2983346	0.86[ASN][1000 genomes]
rs2983349	0.89[ASN][1000 genomes]
rs41427847	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57015168	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57748270	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57999700	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58383805	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58642196	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59510112	0.83[ASN][1000 genomes]
rs59512026	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66546375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67761241	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73332935	0.82[AMR][1000 genomes]
rs910818	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
5	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
11	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
12	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
13	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
15	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
16	chr10:52189800-52194400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr10:52191000-52193400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr10:52191000-52193800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:52191200-52196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:52191400-52200400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:52191600-52193400	Strong transcription	Primary B cells from cord blood	blood
22	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:52191800-52193400	Enhancers	HSMMtube	muscle
25	chr10:52191800-52197000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
28	chr10:52192000-52193600	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:52192000-52196200	Weak transcription	Brain Substantia Nigra	brain
30	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
31	chr10:52192200-52193800	Strong transcription	K562	blood
32	chr10:52192200-52196200	Weak transcription	Primary T cells from cord blood	blood
33	chr10:52192200-52197000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr10:52192400-52194800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:52192400-52196200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:52192400-52196400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:52192400-52196800	Weak transcription	Brain Anterior Caudate	brain
38	chr10:52192400-52196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:52192400-52197000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr10:52192400-52198200	Weak transcription	Right Atrium	heart
41	chr10:52192400-52199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:52192400-52199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:52192400-52200800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:52192400-52202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:52192400-52219400	Weak transcription	Liver	Liver
47	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:52192400-52229400	Weak transcription	Aorta	Aorta

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