Variant report

Variant	rs11188959
Chromosome Location	chr10:98632067-98632068
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	chr10:98624988..98626548-chr10:98631935..98633956,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10437452	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11188937	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188939	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188940	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188947	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188954	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188955	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188956	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188967	1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188971	1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes]
rs11188978	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12241405	0.91[EUR][1000 genomes]
rs12241564	0.87[EUR][1000 genomes]
rs12242330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243551	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244490	0.89[EUR][1000 genomes]
rs12246067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247344	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249427	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249891	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252424	1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256424	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257413	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258355	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258469	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259265	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261278	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261881	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262784	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263331	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264014	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12265242	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266185	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268216	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268272	0.93[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376965	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112175	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs2104785	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183449	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28439735	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	0.86[EUR][1000 genomes]
rs28758432	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56867696	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408003	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57501540	0.91[EUR][1000 genomes]
rs57716318	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	0.81[EUR][1000 genomes]
rs58376960	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59751908	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59938221	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59999388	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576681	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61492214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6584101	0.89[EUR][1000 genomes]
rs7071211	0.93[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs7072273	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073150	0.86[EUR][1000 genomes]
rs7082316	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	0.87[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs7085822	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086875	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7090441	0.91[EUR][1000 genomes]
rs7090690	0.89[EUR][1000 genomes]
rs74153734	0.89[EUR][1000 genomes]
rs7893144	0.83[ASN][1000 genomes]
rs7893325	0.86[EUR][1000 genomes]
rs7893564	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.93[EUR][1000 genomes]
rs7894418	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	0.86[EUR][1000 genomes]
rs7906294	0.93[EUR][1000 genomes]
rs7910221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918085	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920238	0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs7921193	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921216	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11188959	CWF19L1	cis	parietal	SCAN
rs11188959	ENTPD7	cis	cerebellum	SCAN
rs11188959	CCNJ	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98594200-98639400	Weak transcription	Thymus	Thymus
2	chr10:98610800-98632200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:98611000-98649800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr10:98611000-98713000	Weak transcription	Aorta	Aorta
5	chr10:98611200-98640200	Weak transcription	Fetal Heart	heart
6	chr10:98617200-98651600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr10:98619000-98632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:98619000-98643200	Weak transcription	Right Ventricle	heart
9	chr10:98619000-98644200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr10:98619000-98645400	Weak transcription	Dnd41	blood
11	chr10:98620200-98645800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:98620400-98632600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:98622000-98633800	Weak transcription	Brain Germinal Matrix	brain
14	chr10:98622200-98645800	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:98622200-98646000	Weak transcription	Placenta	Placenta
16	chr10:98622400-98632800	Weak transcription	Primary T cells from cord blood	blood
17	chr10:98622400-98638400	Weak transcription	Fetal Thymus	thymus
18	chr10:98622400-98652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:98622600-98640200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr10:98622600-98644200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr10:98622600-98648800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:98622800-98638800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:98623800-98633400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:98624000-98632600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:98624000-98640200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:98624000-98645800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:98624200-98640400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr10:98624400-98632600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:98624400-98637600	Weak transcription	Liver	Liver
30	chr10:98624400-98641600	Weak transcription	Fetal Brain Female	brain
31	chr10:98624400-98644200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:98624400-98645800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:98624400-98645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:98624400-98646000	Weak transcription	Adipose Nuclei	Adipose
35	chr10:98624400-98663000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:98624600-98632800	Weak transcription	Fetal Lung	lung
37	chr10:98624600-98644400	Weak transcription	HSMM	muscle
38	chr10:98624600-98646400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:98624800-98634000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:98624800-98639200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:98624800-98644600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:98624800-98645800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:98624800-98645800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr10:98624800-98649200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:98624800-98649200	Weak transcription	NHEK	skin
46	chr10:98624800-98649800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr10:98624800-98652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:98624800-98656800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:98624800-98696000	Weak transcription	K562	blood
50	chr10:98625000-98632200	Weak transcription	Brain Anterior Caudate	brain

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