Variant report

Variant	rs1341741
Chromosome Location	chr10:888073-888074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:878636..882956-chr10:886285..890248,4	MCF-7	breast:
2	chr10:884410..889606-chr10:890203..894032,6	MCF-7	breast:
3	chr10:887619..890410-chr10:894669..896676,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1013504	0.83[CEU][hapmap]
rs1013505	0.94[CEU][hapmap];0.86[AMR][1000 genomes]
rs10508208	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10904577	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10904581	0.94[CEU][hapmap]
rs10904583	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs10904584	0.94[CEU][hapmap]
rs1106064	0.94[CEU][hapmap]
rs11253444	0.94[CEU][hapmap]
rs11253445	0.94[CEU][hapmap]
rs11253446	0.94[CEU][hapmap]
rs11253458	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253459	0.94[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253460	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253465	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11253467	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253468	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253473	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253475	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11253485	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253488	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11253492	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11253493	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11253494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11253495	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11253499	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11253504	0.81[CEU][hapmap]
rs11253509	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs11253517	0.94[CEU][hapmap];1.00[GIH][hapmap]
rs11253520	0.94[CEU][hapmap]
rs11253521	0.94[CEU][hapmap]
rs11812170	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11812523	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11813210	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11815185	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11816064	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11817793	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11818288	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11818325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12240651	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12244253	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12244355	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12249634	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12249828	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12250936	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12250937	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12251396	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12254002	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12258388	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12259338	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12259801	0.94[CEU][hapmap]
rs12260800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12261911	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12264390	0.94[CEU][hapmap]
rs12264711	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12267709	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12354639	0.94[CEU][hapmap]
rs12357633	0.83[CEU][hapmap]
rs12761424	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12763396	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12764024	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12765174	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12766381	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12768348	0.94[CEU][hapmap]
rs12769002	0.94[CEU][hapmap]
rs12769431	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12769873	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12770190	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12774985	0.94[CEU][hapmap]
rs12778891	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13377166	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341742	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1539174	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs1555899	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17159950	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17159970	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2050944	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34254874	0.80[AMR][1000 genomes]
rs34270014	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34284130	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34405399	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs34847097	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35394603	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35567307	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35637113	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35825568	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35968821	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4522091	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61830929	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61830932	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66631678	0.95[AMR][1000 genomes]
rs7067865	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7074642	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7077278	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72778215	0.95[AMR][1000 genomes]
rs72778229	0.81[EUR][1000 genomes]
rs765867	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7908138	0.94[CEU][hapmap]
rs7914758	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
7	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv466698	chr10:836115-888073	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv549766	chr10:836115-888073	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
19	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong 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	34 gene(s)	inside rSNPs	diseases
20	nsv819263	chr10:888068-889094	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1341741	PFKP	cis	parietal	SCAN
rs1341741	IDI1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:851600-889800	Strong transcription	Dnd41	blood
2	chr10:851600-890800	Strong transcription	Duodenum Mucosa	Duodenum
3	chr10:851600-895600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:851800-894000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:851800-895800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:852200-956400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:852800-891800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:852800-894600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr10:852800-895000	Strong transcription	Fetal Thymus	thymus
10	chr10:856200-892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:865400-890000	Weak transcription	Right Atrium	heart
12	chr10:867400-890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:869000-889400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:869400-890800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:869600-894000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:869600-895200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:869600-896000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr10:870000-892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:870000-892200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr10:870000-896400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr10:870600-892200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr10:870600-959400	Weak transcription	Stomach Mucosa	stomach
23	chr10:872400-889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:873400-895600	Strong transcription	Primary B cells from cord blood	blood
25	chr10:875400-890000	Weak transcription	Fetal Heart	heart
26	chr10:875400-903000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:877600-888800	Weak transcription	NHEK	skin
28	chr10:878600-891600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:878800-890400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr10:878800-890800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:878800-891000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr10:879000-895600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:880000-891600	Strong transcription	Liver	Liver
34	chr10:880000-893200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:880600-888400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr10:881000-890800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr10:882400-888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:883200-889800	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:883200-917200	Weak transcription	Colonic Mucosa	Colon
40	chr10:883600-890000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr10:883800-889800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:883800-889800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:884000-889800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:884000-889800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr10:884000-890400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:884000-890600	Strong transcription	Placenta	Placenta
47	chr10:884000-890800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:884000-892000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:884200-890000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:884200-890800	Strong transcription	NHDF-Ad	bronchial

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