Variant report

Variant	rs10882646
Chromosome Location	chr10:97411725-97411726
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	chr10:97408761..97411732-chr10:97414860..97417411,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000059573	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10159941	0.83[CHB][hapmap]
rs10509687	0.92[CHB][hapmap]
rs10736093	0.94[JPT][hapmap]
rs10748634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748635	0.82[CHB][hapmap]
rs10748637	0.83[CHB][hapmap]
rs10748638	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10748642	0.94[JPT][hapmap]
rs10748643	0.94[JPT][hapmap]
rs10748648	0.85[JPT][hapmap]
rs10786228	0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs10786230	0.83[CHB][hapmap]
rs10786235	0.83[CHB][hapmap]
rs10786236	0.90[JPT][hapmap]
rs10882647	0.82[JPT][hapmap]
rs10882651	0.90[JPT][hapmap]
rs10882652	0.90[JPT][hapmap]
rs10882653	0.83[CHB][hapmap]
rs10882656	0.91[JPT][hapmap]
rs10882657	0.91[JPT][hapmap]
rs10882660	0.90[JPT][hapmap]
rs10882664	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10882665	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10882670	0.83[CHB][hapmap]
rs10882673	0.80[JPT][hapmap]
rs10882675	0.89[JPT][hapmap]
rs10882676	0.80[JPT][hapmap]
rs11188414	0.92[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs11188425	0.81[ASN][1000 genomes]
rs11188459	0.83[CHB][hapmap]
rs11188485	0.83[CHB][hapmap]
rs11188486	0.90[JPT][hapmap]
rs11188488	0.83[CHB][hapmap]
rs11188497	0.88[JPT][hapmap]
rs11596004	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11596976	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12244124	0.81[JPT][hapmap]
rs12244559	0.86[JPT][hapmap]
rs12262943	0.83[CHB][hapmap]
rs1342790	0.90[JPT][hapmap]
rs1342791	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1418709	0.90[JPT][hapmap]
rs1573112	0.94[JPT][hapmap]
rs17111041	0.92[CHB][hapmap]
rs1890186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933165	0.90[JPT][hapmap]
rs1933166	0.83[CHB][hapmap]
rs1933169	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1953710	0.83[CHB][hapmap]
rs2153913	0.90[JPT][hapmap]
rs2185818	0.83[JPT][hapmap]
rs2211002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2225893	0.92[CHB][hapmap]
rs2275273	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2297788	0.86[JPT][hapmap]
rs2485643	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2861147	0.90[JPT][hapmap]
rs2861148	0.89[JPT][hapmap]
rs2861149	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2901873	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2986401	0.85[JPT][hapmap]
rs3176883	0.83[CHB][hapmap]
rs3176891	0.90[JPT][hapmap]
rs3181123	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3181124	0.94[JPT][hapmap]
rs3181129	0.86[JPT][hapmap]
rs3181131	0.94[JPT][hapmap]
rs3750700	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs3750701	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs3793748	0.92[CHB][hapmap]
rs3793749	0.81[JPT][hapmap]
rs3814159	0.94[JPT][hapmap]
rs3929900	0.90[JPT][hapmap]
rs3934409	0.94[JPT][hapmap]
rs3949478	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4074424	0.90[JPT][hapmap]
rs4075310	0.90[JPT][hapmap]
rs4244319	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4290159	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4396219	0.94[JPT][hapmap]
rs4431963	0.94[JPT][hapmap]
rs4457685	0.83[CHB][hapmap]
rs4501930	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4551688	0.94[JPT][hapmap]
rs4582902	0.94[JPT][hapmap]
rs4614366	0.86[JPT][hapmap]
rs479505	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4918950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs4918962	0.90[JPT][hapmap]
rs4918964	0.92[CHB][hapmap]
rs496426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs496641	0.86[EUR][1000 genomes]
rs497331	0.92[CHB][hapmap]
rs5014871	0.90[JPT][hapmap]
rs501819	0.85[JPT][hapmap]
rs535449	0.85[JPT][hapmap]
rs540145	0.82[EUR][1000 genomes]
rs540963	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546138	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs549042	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs571505	0.92[CHB][hapmap]
rs6584022	0.90[JPT][hapmap]
rs6584023	0.91[JPT][hapmap]
rs6584026	0.83[CHB][hapmap]
rs6584027	0.94[JPT][hapmap]
rs6584028	0.83[CHB][hapmap]
rs6584033	0.83[CHB][hapmap]
rs7067762	0.90[JPT][hapmap]
rs7069234	0.83[CHB][hapmap]
rs7071836	0.94[JPT][hapmap]
rs7072572	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7073723	0.83[CHB][hapmap]
rs7074403	0.94[JPT][hapmap]
rs7081414	0.83[CHB][hapmap]
rs7086986	0.91[JPT][hapmap]
rs7088584	0.94[JPT][hapmap]
rs7092594	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7094855	0.82[ASN][1000 genomes]
rs7095587	0.91[JPT][hapmap]
rs7096317	0.85[JPT][hapmap]
rs7893677	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7894648	0.90[JPT][hapmap]
rs7902190	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7905653	0.83[CHB][hapmap]
rs7909569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7915345	0.83[CHB][hapmap]
rs7918235	0.92[CHB][hapmap]
rs7920801	0.83[JPT][hapmap]
rs7920850	0.83[CHB][hapmap]
rs945958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9663413	0.82[JPT][hapmap]
rs9787589	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10882646	ENTPD1	cis	Lymphoblastoid	GTEx
rs10882646	TCTN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97376400-97415200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:97376600-97415000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:97378600-97414200	Weak transcription	Fetal Heart	heart
4	chr10:97389600-97413200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:97389800-97413200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:97399800-97413600	Strong transcription	Dnd41	blood
7	chr10:97400000-97412600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:97401000-97415200	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:97402200-97415200	Weak transcription	Right Ventricle	heart
10	chr10:97402800-97415200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:97403000-97414400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:97403000-97415400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:97404000-97413800	Strong transcription	Fetal Muscle Leg	muscle
14	chr10:97404200-97412600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:97404200-97413000	Strong transcription	HSMM	muscle
16	chr10:97404200-97413200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:97404400-97413000	Strong transcription	NH-A	brain
18	chr10:97404400-97413200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr10:97404600-97412200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr10:97404600-97413800	Strong transcription	Fetal Stomach	stomach
21	chr10:97404800-97415200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:97405800-97412800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr10:97406200-97413000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:97406200-97413200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr10:97406400-97415200	Weak transcription	Brain Angular Gyrus	brain
26	chr10:97407400-97412000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr10:97407600-97414200	Weak transcription	Stomach Mucosa	stomach
28	chr10:97407800-97415400	Weak transcription	Small Intestine	intestine
29	chr10:97408000-97413000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:97408600-97412800	Weak transcription	Aorta	Aorta
31	chr10:97409000-97415200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:97409600-97412200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr10:97409600-97412800	Strong transcription	Ovary	ovary
34	chr10:97409600-97413600	Strong transcription	Hela-S3	cervix
35	chr10:97409800-97412800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr10:97409800-97413200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr10:97409800-97413200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr10:97410000-97411800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:97410000-97411800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr10:97410000-97412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:97410000-97412600	Strong transcription	Fetal Brain Female	brain
42	chr10:97410000-97413000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:97410000-97413200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:97410000-97413200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:97410000-97413200	Strong transcription	HUVEC	blood vessel
46	chr10:97410200-97411800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr10:97410200-97412000	Strong transcription	Brain Anterior Caudate	brain
48	chr10:97410200-97413400	ZNF genes & repeats	GM12878-XiMat	blood
49	chr10:97410200-97413600	Strong transcription	Osteobl	bone
50	chr10:97410600-97413000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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