Variant report

Variant	rs1021103
Chromosome Location	chr3:99603230-99603231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99601088..99603478-chr3:99611897..99614954,3	MCF-7	breast:
2	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
3	chr3:99603110..99605515-chr3:99787025..99789865,2	MCF-7	breast:
4	chr3:99601766..99603960-chr3:99724495..99726434,2	MCF-7	breast:
5	chr3:99602517..99605057-chr7:140621979..140624575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049383	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1016914	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1017968	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs1021102	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs10212525	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs1021341	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1038294	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10511177	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1087198	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs10936005	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10936008	0.91[JPT][hapmap]
rs1287283	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13064704	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13069311	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13317017	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1489816	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs16841679	0.81[CHB][hapmap]
rs1688766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1688772	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1688782	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1718246	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17392948	0.93[CEU][hapmap]
rs2452320	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs2452321	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs28714363	0.82[EUR][1000 genomes]
rs35521705	0.82[EUR][1000 genomes]
rs4075038	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4244711	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4244713	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs4279135	0.82[EUR][1000 genomes]
rs4361315	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs4479633	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4571265	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4928149	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4928232	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4928234	0.83[EUR][1000 genomes]
rs629120	1.00[YRI][hapmap]
rs6440938	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs6765027	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs6790877	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6799379	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6802422	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6806178	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6807176	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6809988	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs694429	1.00[YRI][hapmap]
rs704570	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs704573	0.81[JPT][hapmap]
rs704581	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs704582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704583	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs7609729	1.00[JPT][hapmap]
rs7610486	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7616988	0.94[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7620228	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7629426	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7636447	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs7638900	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs792834	0.93[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs793440	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793445	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793452	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793453	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793457	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793460	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793461	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793462	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793463	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793465	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793466	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793467	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793468	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793470	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793472	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793474	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs793488	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793492	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793494	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793495	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793503	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs796977	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs796978	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs809415	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs812657	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs923470	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs923471	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9810235	0.82[EUR][1000 genomes]
rs9814359	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9815439	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9823908	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9832186	0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs9833888	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9833980	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9841186	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9851645	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9852435	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9864437	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9872871	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs9873709	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9873878	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs9875640	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9878931	0.82[EUR][1000 genomes]

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	nsv822194	chr3:99600260-99604375	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1021103	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595400-99603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:99595400-99603400	Weak transcription	Small Intestine	intestine
3	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:99597000-99603400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:99597200-99603400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:99597200-99614200	Weak transcription	HMEC	breast
10	chr3:99597800-99603400	Weak transcription	GM12878-XiMat	blood
11	chr3:99600600-99603400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
13	chr3:99601600-99603400	Weak transcription	Adipose Nuclei	Adipose
14	chr3:99601800-99604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:99602000-99604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:99602000-99605400	Enhancers	HepG2	liver
17	chr3:99602400-99604200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:99602600-99604200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:99602600-99604600	Enhancers	Primary T cells from cord blood	blood
20	chr3:99602600-99604800	Enhancers	Fetal Intestine Large	intestine
21	chr3:99602600-99605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:99602800-99604000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:99602800-99604000	Enhancers	K562	blood
24	chr3:99602800-99604200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:99602800-99604200	Enhancers	NHEK	skin
26	chr3:99602800-99604600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:99603000-99603400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:99603000-99603400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:99603000-99603400	Weak transcription	Psoas Muscle	Psoas
30	chr3:99603000-99603800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:99603000-99604000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:99603000-99604200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:99603000-99604200	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:99603000-99604400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:99603000-99605400	Enhancers	Stomach Mucosa	stomach
36	chr3:99603200-99603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:99603200-99603400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:99603200-99603600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:99603200-99603600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:99603200-99603600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:99603200-99603800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:99603200-99603800	Flanking Active TSS	HUVEC	blood vessel
43	chr3:99603200-99604000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:99603200-99604000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:99603200-99604000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:99603200-99604200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:99603200-99604200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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