Variant report

Variant	rs11188417
Chromosome Location	chr10:97411680-97411681
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: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10509686	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs1053905	0.85[CHB][hapmap]
rs10786227	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10882638	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs10882640	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs10882641	0.85[CHB][hapmap]
rs10882643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882650	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882654	0.85[CHB][hapmap]
rs10882671	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs11188393	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188394	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188396	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188397	0.85[CHB][hapmap]
rs11188398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188399	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11188400	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188404	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188406	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188437	0.83[EUR][1000 genomes]
rs11188444	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11188455	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11188464	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11188484	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs11188504	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs11591779	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592213	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593044	0.86[AMR][1000 genomes]
rs11597321	0.86[AMR][1000 genomes]
rs12354848	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12357173	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12358481	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12359272	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12359366	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1270505	0.84[MEX][hapmap]
rs12778814	0.85[CHB][hapmap]
rs1340837	0.81[CEU][hapmap]
rs1409709	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs17461546	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17462179	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17553401	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1891536	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs2004611	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017218	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152916	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2296689	0.85[CHB][hapmap]
rs2296691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296692	0.85[CHB][hapmap]
rs2861151	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3176895	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs3181122	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs3763707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4037	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320886	0.84[AMR][1000 genomes]
rs4417206	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568937	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4917697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918955	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918966	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs526928	0.84[MEX][hapmap]
rs55801606	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56322409	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57347444	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869573	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61871790	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61871792	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61871793	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61871796	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6946	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7072953	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7073010	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7086071	0.80[MEX][hapmap]
rs7089668	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs749050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917792	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918339	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7918947	0.80[MEX][hapmap]
rs8758	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943342	0.85[CHB][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11188417	FRAT2	cis	cerebellum	SCAN
rs11188417	ENTPD1	cis	multi-tissue	Pritchard
rs11188417	NOC3L	cis	cerebellum	SCAN
rs11188417	ALDH18A1	cis	cerebellum	SCAN
rs11188417	ENTPD1	cis	lymphoblastoid	seeQTL

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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