Variant report

Variant	rs9872871
Chromosome Location	chr3:99658702-99658703
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99653473..99655076-chr3:99658012..99659840,2	MCF-7	breast:
2	chr3:99658541..99660267-chr3:99661870..99663400,2	K562	blood:
3	chr3:99657995..99660872-chr3:99661118..99663012,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10049383	0.91[JPT][hapmap]
rs1016914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017968	0.89[JPT][hapmap]
rs1021102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021103	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs10212525	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1021341	0.91[JPT][hapmap]
rs1038294	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs10511177	0.91[JPT][hapmap]
rs1059905	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1087198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936008	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1287283	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13064704	0.91[JPT][hapmap]
rs13069311	0.91[JPT][hapmap]
rs13317017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323143	0.91[JPT][hapmap]
rs1489816	0.82[JPT][hapmap]
rs1688766	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1688771	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1688774	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174947	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718244	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1718245	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2452320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075038	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4244711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244713	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4361315	0.91[JPT][hapmap]
rs4479633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4571265	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4928232	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62283523	0.83[AMR][1000 genomes]
rs6440938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765027	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790535	0.91[JPT][hapmap]
rs6790877	0.90[JPT][hapmap]
rs6799379	0.91[JPT][hapmap]
rs6802422	0.91[JPT][hapmap]
rs6803204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806178	0.91[JPT][hapmap]
rs6807176	0.91[JPT][hapmap]
rs68092024	0.94[AFR][1000 genomes]
rs6809988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694429	0.89[YRI][hapmap]
rs704570	0.91[JPT][hapmap];0.90[YRI][hapmap]
rs704573	0.91[JPT][hapmap]
rs704575	0.83[JPT][hapmap]
rs704578	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704579	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704581	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704582	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs704583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609729	0.90[JPT][hapmap]
rs7610486	0.91[JPT][hapmap]
rs7616988	0.82[JPT][hapmap]
rs7620228	0.91[JPT][hapmap]
rs7627991	0.91[JPT][hapmap]
rs7629426	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792834	0.82[JPT][hapmap];0.89[YRI][hapmap]
rs792840	0.82[JPT][hapmap]
rs792841	0.82[JPT][hapmap]
rs793440	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793442	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793445	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793447	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793448	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793449	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793453	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793455	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793458	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793459	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793470	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793471	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793479	0.81[JPT][hapmap]
rs793492	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793494	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793496	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793499	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793501	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793503	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796978	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs809415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923470	0.91[JPT][hapmap]
rs923471	0.91[JPT][hapmap]
rs9814359	0.91[JPT][hapmap]
rs9815439	0.90[JPT][hapmap]
rs9817005	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823908	0.91[JPT][hapmap]
rs9828079	0.91[JPT][hapmap]
rs9833888	0.91[JPT][hapmap]
rs9833980	0.91[JPT][hapmap]
rs9837602	0.83[JPT][hapmap]
rs9841186	0.91[JPT][hapmap]
rs9851645	0.91[JPT][hapmap]
rs9864437	0.91[JPT][hapmap]
rs9873709	0.91[JPT][hapmap]
rs9873878	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9875640	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9872871	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
2	chr3:99648800-99663200	Weak transcription	Gastric	stomach
3	chr3:99648800-99664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:99649600-99662800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:99650400-99663000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:99650400-99667400	Weak transcription	A549	lung
7	chr3:99650600-99662800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:99650600-99663200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:99654000-99663000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:99654600-99659400	Weak transcription	Right Atrium	heart
11	chr3:99654600-99664000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:99654800-99663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:99654800-99663000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:99654800-99663000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:99654800-99663200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:99655200-99663000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:99656000-99658800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:99656200-99659400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:99656200-99659800	Enhancers	Rectal Smooth Muscle	rectum
20	chr3:99656200-99660600	Enhancers	Stomach Mucosa	stomach
21	chr3:99656400-99659200	Enhancers	Fetal Intestine Small	intestine
22	chr3:99656400-99659600	Enhancers	Fetal Stomach	stomach
23	chr3:99656400-99660000	Enhancers	Colon Smooth Muscle	Colon
24	chr3:99656600-99659000	Enhancers	Fetal Lung	lung
25	chr3:99656600-99662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:99656800-99659800	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:99657200-99658800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:99657200-99659000	Weak transcription	Aorta	Aorta
29	chr3:99657200-99662600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:99657400-99663000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:99657400-99663200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:99657600-99662600	Weak transcription	Brain Germinal Matrix	brain
33	chr3:99657600-99663000	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
35	chr3:99657800-99660000	Enhancers	HepG2	liver
36	chr3:99657800-99662800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:99657800-99662800	Weak transcription	Fetal Heart	heart
38	chr3:99657800-99662800	Weak transcription	HSMMtube	muscle
39	chr3:99657800-99662800	Weak transcription	NHDF-Ad	bronchial
40	chr3:99657800-99663000	Weak transcription	Fetal Brain Male	brain
41	chr3:99657800-99663000	Weak transcription	NHEK	skin
42	chr3:99657800-99663400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:99657800-99663400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:99657800-99664200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:99657800-99664200	Weak transcription	Fetal Brain Female	brain
46	chr3:99658000-99660400	Enhancers	Ovary	ovary
47	chr3:99658000-99663000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:99658200-99661800	Weak transcription	Psoas Muscle	Psoas
49	chr3:99658200-99662600	Weak transcription	Left Ventricle	heart
50	chr3:99658200-99662800	Weak transcription	NH-A	brain

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