Variant report

Variant	rs10049383
Chromosome Location	chr3:99748548-99748549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99746722..99749482-chr3:99759616..99761759,2	MCF-7	breast:
2	chr3:99741319..99743139-chr3:99748165..99750114,2	K562	blood:
3	chr3:99744838..99746537-chr3:99747775..99750213,2	MCF-7	breast:
4	chr3:99697715..99700181-chr3:99746878..99748971,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1016914	0.91[JPT][hapmap]
rs1017968	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021102	0.90[JPT][hapmap]
rs1021103	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10212525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021341	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10511177	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936005	0.91[JPT][hapmap]
rs10936008	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13064704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093838	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13317017	0.91[JPT][hapmap]
rs13323143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1489816	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16841920	0.81[CHB][hapmap]
rs1688766	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1688782	0.91[JPT][hapmap]
rs17379739	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17392948	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17393059	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291494	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291495	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2315840	0.81[CHB][hapmap]
rs2452320	0.91[JPT][hapmap]
rs2452321	0.91[JPT][hapmap]
rs28503408	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28714363	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28870092	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34922392	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34996634	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35154249	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35521705	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35669453	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35844878	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35885423	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4244711	0.91[JPT][hapmap]
rs4244713	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4279135	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4361315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4479633	0.91[JPT][hapmap]
rs4571265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928149	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4928232	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4928234	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285461	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285462	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285471	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285473	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285478	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440938	0.91[JPT][hapmap]
rs6765027	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6790535	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799379	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806178	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807176	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809988	0.91[JPT][hapmap]
rs704581	0.81[JPT][hapmap]
rs704582	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs704583	0.91[JPT][hapmap]
rs71313585	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609729	1.00[JPT][hapmap]
rs7610486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7616988	0.94[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7620228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629426	0.91[JPT][hapmap]
rs7636447	0.91[JPT][hapmap]
rs7638900	0.91[JPT][hapmap]
rs793440	0.91[JPT][hapmap]
rs793445	0.91[JPT][hapmap]
rs793460	0.91[JPT][hapmap]
rs793461	0.91[JPT][hapmap]
rs793462	0.91[JPT][hapmap]
rs793463	0.91[JPT][hapmap]
rs793465	0.91[JPT][hapmap]
rs793466	0.91[JPT][hapmap]
rs793499	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs793503	0.91[JPT][hapmap]
rs796977	0.90[JPT][hapmap]
rs796978	0.91[JPT][hapmap]
rs809415	0.91[JPT][hapmap]
rs812657	0.91[JPT][hapmap]
rs923470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289985	0.80[CEU][hapmap]
rs9810235	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9814359	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815439	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832186	0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834484	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852435	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853823	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854260	0.87[CEU][hapmap]
rs9860290	0.87[CEU][hapmap]
rs9864437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872871	0.91[JPT][hapmap]
rs9873709	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875640	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875664	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875878	0.80[CEU][hapmap]
rs9878931	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10049383	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:99735600-99750400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
7	chr3:99742200-99751000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
9	chr3:99742600-99749200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:99743000-99750800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:99743800-99748800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:99743800-99749000	Weak transcription	HMEC	breast
13	chr3:99743800-99751000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:99743800-99751200	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:99743800-99752200	Weak transcription	A549	lung
16	chr3:99743800-99759200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:99744000-99748600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:99744000-99753200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:99744200-99748600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:99744200-99748600	Weak transcription	HSMMtube	muscle
21	chr3:99744200-99748800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:99744200-99750800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:99744200-99753000	Weak transcription	Fetal Kidney	kidney
24	chr3:99744200-99759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:99744400-99749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:99744400-99753000	Weak transcription	HepG2	liver
27	chr3:99744600-99750400	Weak transcription	NH-A	brain
28	chr3:99744600-99750400	Weak transcription	Osteobl	bone
29	chr3:99744800-99748800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:99744800-99751000	Weak transcription	NHDF-Ad	bronchial
31	chr3:99744800-99751200	Weak transcription	Ovary	ovary
32	chr3:99745200-99748600	Weak transcription	Stomach Mucosa	stomach
33	chr3:99745200-99751800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:99745800-99749600	Enhancers	K562	blood
35	chr3:99746000-99748800	Weak transcription	NHEK	skin
36	chr3:99746000-99758800	Weak transcription	Left Ventricle	heart
37	chr3:99746400-99748800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:99746400-99751200	Weak transcription	Pancreas	Pancrea
39	chr3:99746600-99751000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:99746800-99750200	Weak transcription	Psoas Muscle	Psoas
42	chr3:99746800-99750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:99746800-99752000	Weak transcription	HUVEC	blood vessel
44	chr3:99747000-99749000	Enhancers	Fetal Intestine Large	intestine
45	chr3:99747200-99748600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:99747600-99749000	Enhancers	Fetal Intestine Small	intestine
47	chr3:99748200-99753600	Enhancers	HSMM	muscle
48	chr3:99748400-99748600	Enhancers	GM12878-XiMat	blood
49	chr3:99748400-99748800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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